From 4d73bd8cf9715a2a5d7b548411ede2de74c4a96f Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 31 Oct 2024 11:21:16 +0100 Subject: [PATCH 01/59] bump gatk4 --- .../nf-core/gatk4/addorreplacereadgroups/environment.yml | 2 +- modules/nf-core/gatk4/addorreplacereadgroups/main.nf | 4 ++-- modules/nf-core/gatk4/annotateintervals/environment.yml | 2 +- modules/nf-core/gatk4/annotateintervals/main.nf | 4 ++-- modules/nf-core/gatk4/applybqsr/environment.yml | 2 +- modules/nf-core/gatk4/applybqsr/main.nf | 4 ++-- modules/nf-core/gatk4/applyvqsr/environment.yml | 2 +- modules/nf-core/gatk4/applyvqsr/main.nf | 4 ++-- modules/nf-core/gatk4/asereadcounter/environment.yml | 2 +- modules/nf-core/gatk4/asereadcounter/main.nf | 4 ++-- modules/nf-core/gatk4/baserecalibrator/environment.yml | 2 +- modules/nf-core/gatk4/baserecalibrator/main.nf | 4 ++-- modules/nf-core/gatk4/bedtointervallist/environment.yml | 2 +- modules/nf-core/gatk4/bedtointervallist/main.nf | 4 ++-- .../nf-core/gatk4/calculatecontamination/environment.yml | 2 +- modules/nf-core/gatk4/calculatecontamination/main.nf | 4 ++-- modules/nf-core/gatk4/calibratedragstrmodel/environment.yml | 2 +- modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 4 ++-- modules/nf-core/gatk4/collectreadcounts/environment.yml | 2 +- modules/nf-core/gatk4/collectreadcounts/main.nf | 4 ++-- modules/nf-core/gatk4/collectsvevidence/environment.yml | 2 +- modules/nf-core/gatk4/collectsvevidence/main.nf | 4 ++-- modules/nf-core/gatk4/combinegvcfs/environment.yml | 2 +- modules/nf-core/gatk4/combinegvcfs/main.nf | 4 ++-- modules/nf-core/gatk4/composestrtablefile/environment.yml | 2 +- modules/nf-core/gatk4/composestrtablefile/main.nf | 4 ++-- modules/nf-core/gatk4/condensedepthevidence/environment.yml | 2 +- modules/nf-core/gatk4/condensedepthevidence/main.nf | 4 ++-- .../gatk4/createreadcountpanelofnormals/environment.yml | 2 +- modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf | 4 ++-- .../nf-core/gatk4/createsequencedictionary/environment.yml | 2 +- modules/nf-core/gatk4/createsequencedictionary/main.nf | 4 ++-- .../gatk4/createsomaticpanelofnormals/environment.yml | 2 +- modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 4 ++-- modules/nf-core/gatk4/denoisereadcounts/environment.yml | 2 +- modules/nf-core/gatk4/denoisereadcounts/main.nf | 4 ++-- .../gatk4/determinegermlinecontigploidy/environment.yml | 5 +++++ modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf | 6 ++++-- .../nf-core/gatk4/estimatelibrarycomplexity/environment.yml | 2 +- modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 4 ++-- modules/nf-core/gatk4/fastqtosam/environment.yml | 2 +- modules/nf-core/gatk4/fastqtosam/main.nf | 4 ++-- modules/nf-core/gatk4/filterintervals/environment.yml | 2 +- modules/nf-core/gatk4/filterintervals/main.nf | 4 ++-- modules/nf-core/gatk4/filtermutectcalls/environment.yml | 2 +- modules/nf-core/gatk4/filtermutectcalls/main.nf | 4 ++-- modules/nf-core/gatk4/filtervarianttranches/environment.yml | 2 +- modules/nf-core/gatk4/filtervarianttranches/main.nf | 4 ++-- modules/nf-core/gatk4/gatherbqsrreports/environment.yml | 2 +- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 4 ++-- modules/nf-core/gatk4/gatherpileupsummaries/environment.yml | 2 +- modules/nf-core/gatk4/gatherpileupsummaries/main.nf | 4 ++-- modules/nf-core/gatk4/genomicsdbimport/environment.yml | 2 +- modules/nf-core/gatk4/genomicsdbimport/main.nf | 4 ++-- modules/nf-core/gatk4/genotypegvcfs/environment.yml | 2 +- modules/nf-core/gatk4/genotypegvcfs/main.nf | 4 ++-- modules/nf-core/gatk4/germlinecnvcaller/environment.yml | 5 +++++ modules/nf-core/gatk4/germlinecnvcaller/main.nf | 6 ++++-- modules/nf-core/gatk4/getpileupsummaries/environment.yml | 2 +- modules/nf-core/gatk4/getpileupsummaries/main.nf | 4 ++-- modules/nf-core/gatk4/haplotypecaller/environment.yml | 2 +- modules/nf-core/gatk4/haplotypecaller/main.nf | 4 ++-- modules/nf-core/gatk4/indexfeaturefile/environment.yml | 2 +- modules/nf-core/gatk4/indexfeaturefile/main.nf | 4 ++-- modules/nf-core/gatk4/intervallisttobed/environment.yml | 2 +- modules/nf-core/gatk4/intervallisttobed/main.nf | 4 ++-- modules/nf-core/gatk4/intervallisttools/environment.yml | 2 +- modules/nf-core/gatk4/intervallisttools/main.nf | 4 ++-- .../nf-core/gatk4/learnreadorientationmodel/environment.yml | 2 +- modules/nf-core/gatk4/learnreadorientationmodel/main.nf | 4 ++-- .../nf-core/gatk4/leftalignandtrimvariants/environment.yml | 2 +- modules/nf-core/gatk4/leftalignandtrimvariants/main.nf | 4 ++-- modules/nf-core/gatk4/markduplicates/environment.yml | 2 +- modules/nf-core/gatk4/mergebamalignment/environment.yml | 2 +- modules/nf-core/gatk4/mergebamalignment/main.nf | 4 ++-- modules/nf-core/gatk4/mergemutectstats/environment.yml | 2 +- modules/nf-core/gatk4/mergemutectstats/main.nf | 4 ++-- modules/nf-core/gatk4/mergevcfs/environment.yml | 2 +- modules/nf-core/gatk4/mergevcfs/main.nf | 4 ++-- modules/nf-core/gatk4/mutect2/environment.yml | 2 +- modules/nf-core/gatk4/mutect2/main.nf | 4 ++-- modules/nf-core/gatk4/preprocessintervals/environment.yml | 2 +- modules/nf-core/gatk4/preprocessintervals/main.nf | 4 ++-- modules/nf-core/gatk4/printreads/environment.yml | 2 +- modules/nf-core/gatk4/printreads/main.nf | 4 ++-- modules/nf-core/gatk4/printsvevidence/environment.yml | 2 +- modules/nf-core/gatk4/printsvevidence/main.nf | 4 ++-- modules/nf-core/gatk4/reblockgvcf/environment.yml | 2 +- modules/nf-core/gatk4/reblockgvcf/main.nf | 4 ++-- modules/nf-core/gatk4/revertsam/environment.yml | 2 +- modules/nf-core/gatk4/revertsam/main.nf | 4 ++-- modules/nf-core/gatk4/samtofastq/environment.yml | 2 +- modules/nf-core/gatk4/samtofastq/main.nf | 4 ++-- modules/nf-core/gatk4/selectvariants/environment.yml | 2 +- modules/nf-core/gatk4/selectvariants/main.nf | 4 ++-- modules/nf-core/gatk4/shiftfasta/environment.yml | 2 +- modules/nf-core/gatk4/shiftfasta/main.nf | 4 ++-- modules/nf-core/gatk4/sitedepthtobaf/environment.yml | 2 +- modules/nf-core/gatk4/sitedepthtobaf/main.nf | 4 ++-- modules/nf-core/gatk4/splitcram/environment.yml | 2 +- modules/nf-core/gatk4/splitcram/main.nf | 4 ++-- modules/nf-core/gatk4/splitintervals/environment.yml | 2 +- modules/nf-core/gatk4/splitintervals/main.nf | 4 ++-- modules/nf-core/gatk4/splitncigarreads/environment.yml | 2 +- modules/nf-core/gatk4/splitncigarreads/main.nf | 4 ++-- modules/nf-core/gatk4/svannotate/environment.yml | 2 +- modules/nf-core/gatk4/svannotate/main.nf | 4 ++-- modules/nf-core/gatk4/svcluster/environment.yml | 2 +- modules/nf-core/gatk4/svcluster/main.nf | 4 ++-- modules/nf-core/gatk4/variantfiltration/environment.yml | 2 +- modules/nf-core/gatk4/variantfiltration/main.nf | 4 ++-- modules/nf-core/gatk4/variantrecalibrator/environment.yml | 2 +- modules/nf-core/gatk4/variantrecalibrator/main.nf | 4 ++-- modules/nf-core/gatk4/variantstotable/environment.yml | 2 +- modules/nf-core/gatk4/variantstotable/main.nf | 4 ++-- 115 files changed, 184 insertions(+), 170 deletions(-) create mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/environment.yml diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf index 861f7045a14..8e0142f943d 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf +++ b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf @@ -4,8 +4,8 @@ process GATK4_ADDORREPLACEREADGROUPS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/annotateintervals/main.nf b/modules/nf-core/gatk4/annotateintervals/main.nf index dfe9dc27a09..e48156d79ec 100644 --- a/modules/nf-core/gatk4/annotateintervals/main.nf +++ b/modules/nf-core/gatk4/annotateintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_ANNOTATEINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 4e91c311b0e..7dae410c685 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYBQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 047321b8e9e..e14649aab58 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYVQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/asereadcounter/environment.yml +++ b/modules/nf-core/gatk4/asereadcounter/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf b/modules/nf-core/gatk4/asereadcounter/main.nf index cb9083e0761..87cd0cce29f 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf +++ b/modules/nf-core/gatk4/asereadcounter/main.nf @@ -4,8 +4,8 @@ process GATK4_ASEREADCOUNTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 1a299862657..3c321159377 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_BASERECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 68863d677d7..43db8839ab6 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -4,8 +4,8 @@ process GATK4_BEDTOINTERVALLIST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 1ca3fd9d45f..52f5d194b39 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -4,8 +4,8 @@ process GATK4_CALCULATECONTAMINATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 88e108cb01e..7e8f50e21df 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam), path(bam_index) diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 2c545d22432..7007d28bfef 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -4,8 +4,8 @@ process GATK4_COLLECTREADCOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectsvevidence/environment.yml b/modules/nf-core/gatk4/collectsvevidence/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/collectsvevidence/environment.yml +++ b/modules/nf-core/gatk4/collectsvevidence/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 9e6dd4a284b..47c264108c1 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_COLLECTSVEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(site_depth_vcf), path(site_depth_vcf_tbi) diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 56db0c12c86..8b66e3eef7d 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_COMBINEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 5073ab64200..b6e2ef65a89 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -4,8 +4,8 @@ process GATK4_COMPOSESTRTABLEFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: path(fasta) diff --git a/modules/nf-core/gatk4/condensedepthevidence/environment.yml b/modules/nf-core/gatk4/condensedepthevidence/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/environment.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/condensedepthevidence/main.nf b/modules/nf-core/gatk4/condensedepthevidence/main.nf index a37b6693f39..0313b46b635 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/main.nf +++ b/modules/nf-core/gatk4/condensedepthevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_CONDENSEDEPTHEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(depth_evidence), path(depth_evidence_index) diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf index 332f9d9247f..a31a20d0b44 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATEREADCOUNTPANELOFNORMALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(counts) diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index c7f1d75b3c1..e42735af6b1 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESEQUENCEDICTIONARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 27a50dc208d..ffd77888ed0 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESOMATICPANELOFNORMALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(genomicsdb) diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/denoisereadcounts/main.nf b/modules/nf-core/gatk4/denoisereadcounts/main.nf index 878e85c6f97..3d4637d8539 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/main.nf +++ b/modules/nf-core/gatk4/denoisereadcounts/main.nf @@ -4,8 +4,8 @@ process GATK4_DENOISEREADCOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(counts) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml new file mode 100644 index 00000000000..e93eac37506 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index 71a67f70320..97a4f5a6269 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -3,8 +3,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(counts), path(bed), path(exclude_beds) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index e0744e16f7d..31430a94291 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -4,8 +4,8 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/gatk4/fastqtosam/environment.yml b/modules/nf-core/gatk4/fastqtosam/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/fastqtosam/environment.yml +++ b/modules/nf-core/gatk4/fastqtosam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 452d1ca1f35..acd0e71a527 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -4,8 +4,8 @@ process GATK4_FASTQTOSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filterintervals/main.nf b/modules/nf-core/gatk4/filterintervals/main.nf index bf1f3a0e369..c2a3ccfc4a1 100644 --- a/modules/nf-core/gatk4/filterintervals/main.nf +++ b/modules/nf-core/gatk4/filterintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 0532ec02582..927c514ebd6 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERMUTECTCALLS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 05489e179b9..2730938769e 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERVARIANTTRANCHES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 79667a29948..98a71473c2c 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -4,8 +4,8 @@ process GATK4_GATHERBQSRREPORTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index bcafd544b43..36f1a4123d8 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GATHERPILEUPSUMMARIES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 6f1d4c53709..ce9a7042378 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOMICSDBIMPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index f180f74975c..a0fed0699ac 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOTYPEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml new file mode 100644 index 00000000000..e93eac37506 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index cd1916ec439..180c0a940f9 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -2,8 +2,10 @@ process GATK4_GERMLINECNVCALLER { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(tsv), path(intervals), path(ploidy), path(model) diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 43611271e01..af477f818e7 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GETPILEUPSUMMARIES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index b2aff48969e..097626064ce 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -4,8 +4,8 @@ process GATK4_HAPLOTYPECALLER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index b1a2698c263..dddb2c111fc 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -4,8 +4,8 @@ process GATK4_INDEXFEATUREFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 2f6893c0caf..61f68a68dcf 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOBED { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 400fa0380e7..5bf38ab8aad 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOOLS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index a61b292812e..2d15b176023 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_LEARNREADORIENTATIONMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index b0bede7093d..0fbccc1a5b3 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -4,8 +4,8 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 3c73c17e433..8a70182eac7 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -3,6 +3,6 @@ channels: - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 - bioconda::htslib=1.19.1 - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 0085026c8e5..f390eda2317 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEBAMALIGNMENT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 06bce31e31b..1a500fc1f88 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEMUTECTSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 9e8d43915cc..d9ae935d5f8 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 79d8d2826ca..044da1822f9 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -4,8 +4,8 @@ process GATK4_MUTECT2 { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/preprocessintervals/main.nf b/modules/nf-core/gatk4/preprocessintervals/main.nf index dffc4bb1df8..0a606275e77 100644 --- a/modules/nf-core/gatk4/preprocessintervals/main.nf +++ b/modules/nf-core/gatk4/preprocessintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_PREPROCESSINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf index f97180adc24..e24cfa49fb7 100644 --- a/modules/nf-core/gatk4/printreads/main.nf +++ b/modules/nf-core/gatk4/printreads/main.nf @@ -4,8 +4,8 @@ process GATK4_PRINTREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/printsvevidence/environment.yml b/modules/nf-core/gatk4/printsvevidence/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/printsvevidence/environment.yml +++ b/modules/nf-core/gatk4/printsvevidence/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 5cf5b05affc..c4e42bbc5eb 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_PRINTSVEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(evidence_files), path(evidence_indices) diff --git a/modules/nf-core/gatk4/reblockgvcf/environment.yml b/modules/nf-core/gatk4/reblockgvcf/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/reblockgvcf/environment.yml +++ b/modules/nf-core/gatk4/reblockgvcf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 4b58bec7788..43376050cb6 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -4,8 +4,8 @@ process GATK4_REBLOCKGVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 635784ab29f..5ce72543e21 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -4,8 +4,8 @@ process GATK4_REVERTSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 35b9b76db4c..2b1484e7da5 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -4,8 +4,8 @@ process GATK4_SAMTOFASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/environment.yml b/modules/nf-core/gatk4/selectvariants/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/selectvariants/environment.yml +++ b/modules/nf-core/gatk4/selectvariants/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index c342ee93996..4e59b3ef9cb 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -4,8 +4,8 @@ process GATK4_SELECTVARIANTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_idx), path (intervals) diff --git a/modules/nf-core/gatk4/shiftfasta/environment.yml b/modules/nf-core/gatk4/shiftfasta/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/shiftfasta/environment.yml +++ b/modules/nf-core/gatk4/shiftfasta/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/shiftfasta/main.nf b/modules/nf-core/gatk4/shiftfasta/main.nf index 350ff8d3366..8d6874ff6aa 100644 --- a/modules/nf-core/gatk4/shiftfasta/main.nf +++ b/modules/nf-core/gatk4/shiftfasta/main.nf @@ -4,8 +4,8 @@ process GATK4_SHIFTFASTA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/sitedepthtobaf/main.nf b/modules/nf-core/gatk4/sitedepthtobaf/main.nf index 514096cac47..b7d7c9eac61 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/main.nf +++ b/modules/nf-core/gatk4/sitedepthtobaf/main.nf @@ -4,8 +4,8 @@ process GATK4_SITEDEPTHTOBAF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(site_depths), path(site_depths_indices) diff --git a/modules/nf-core/gatk4/splitcram/environment.yml b/modules/nf-core/gatk4/splitcram/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/splitcram/environment.yml +++ b/modules/nf-core/gatk4/splitcram/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitcram/main.nf b/modules/nf-core/gatk4/splitcram/main.nf index 1e635cd4926..48544298ab8 100644 --- a/modules/nf-core/gatk4/splitcram/main.nf +++ b/modules/nf-core/gatk4/splitcram/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITCRAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(cram) diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index d59b6afb1d7..db43dfa19c9 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index e2c287a02b1..b5552391ea4 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITNCIGARREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/svannotate/environment.yml +++ b/modules/nf-core/gatk4/svannotate/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svannotate/main.nf b/modules/nf-core/gatk4/svannotate/main.nf index e5cf874a2b9..e76d81c16a7 100644 --- a/modules/nf-core/gatk4/svannotate/main.nf +++ b/modules/nf-core/gatk4/svannotate/main.nf @@ -4,8 +4,8 @@ process GATK4_SVANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(bed) diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/svcluster/environment.yml +++ b/modules/nf-core/gatk4/svcluster/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svcluster/main.nf b/modules/nf-core/gatk4/svcluster/main.nf index 855dd700f89..19bd55c63be 100644 --- a/modules/nf-core/gatk4/svcluster/main.nf +++ b/modules/nf-core/gatk4/svcluster/main.nf @@ -4,8 +4,8 @@ process GATK4_SVCLUSTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcfs), path(indices) diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index 388c60abf0e..b23f6cf4e9d 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTFILTRATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 24844ce0c95..317b83ce60a 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTRECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gatk4/variantstotable/environment.yml b/modules/nf-core/gatk4/variantstotable/environment.yml index aa7d804d4ad..03610def61e 100644 --- a/modules/nf-core/gatk4/variantstotable/environment.yml +++ b/modules/nf-core/gatk4/variantstotable/environment.yml @@ -3,4 +3,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantstotable/main.nf b/modules/nf-core/gatk4/variantstotable/main.nf index 5a189beed61..b61040aac48 100644 --- a/modules/nf-core/gatk4/variantstotable/main.nf +++ b/modules/nf-core/gatk4/variantstotable/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTSTOTABLE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(arguments_file), path(include_intervals), path(exclude_intervals) From c581acf54846673c6951c38f1320de06a85335bc Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 31 Oct 2024 10:46:00 +0000 Subject: [PATCH 02/59] fix some tests --- .../tests/main.nf.test.snap | 18 +++--- .../annotateintervals/tests/main.nf.test.snap | 58 +++++++++---------- .../gatk4/applybqsr/tests/main.nf.test.snap | 56 +++++++++--------- .../gatk4/applyvqsr/tests/main.nf.test.snap | 26 ++++----- .../gatk4/asereadcounter/main.nf.test.snap | 10 ++-- .../baserecalibrator/tests/main.nf.test.snap | 50 ++++++++-------- .../bedtointervallist/tests/main.nf.test.snap | 10 ++-- .../tests/main.nf.test.snap | 34 +++++------ .../tests/main.nf.test.snap | 32 +++++----- .../collectreadcounts/tests/main.nf.test.snap | 20 +++---- .../denoisereadcounts/tests/main.nf.test.snap | 8 +-- .../intervallisttools/tests/main.nf.test.snap | 20 +++---- 12 files changed, 171 insertions(+), 171 deletions(-) diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap index 93a87cc39eb..07101dc9bfd 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap @@ -32,7 +32,7 @@ ], "3": [ - "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + "versions.yml:md5,09f498302943b70029a56ddf65522814" ], "bai": [ [ @@ -54,27 +54,27 @@ ], "versions": [ - "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + "versions.yml:md5,09f498302943b70029a56ddf65522814" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T13:19:33.815262" + "timestamp": "2024-10-31T10:28:22.832793576" }, "versions": { "content": [ [ - "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + "versions.yml:md5,09f498302943b70029a56ddf65522814" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T13:19:18.103325" + "timestamp": "2024-10-31T10:28:10.146204216" }, "cram_name": { "content": [ diff --git a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap index 749f6fb6f13..3b06f09771a 100644 --- a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:07:36.32193" + "timestamp": "2024-10-31T10:29:29.006068994" }, "homo_sapiens genome [interval_list]": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:08:12.533176" + "timestamp": "2024-10-31T10:30:08.763305448" }, "homo_sapiens genome multi-interval [bed]": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:07:54.643276" + "timestamp": "2024-10-31T10:29:48.403638052" }, "homo_sapiens genome [interval_list] mappable_regions": { "content": [ @@ -117,7 +117,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -129,28 +129,28 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:08:31.311782" + "timestamp": "2024-10-31T10:30:23.256626974" }, "homo_sapiens genome [bed] - stub": { "content": [ [ "test.tsv", - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:09:04.54745" + "timestamp": "2024-10-31T10:30:52.179735439" }, "homo_sapiens genome [interval_list] duplication_regions": { "content": [ @@ -165,7 +165,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -177,14 +177,14 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:08:49.684766" + "timestamp": "2024-10-31T10:30:37.398809104" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap index 19b37d0636d..427cbddb8d0 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ @@ -28,15 +28,15 @@ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:25:00.314573" + "timestamp": "2024-10-31T10:32:45.888751339" }, "sarscov2 - bam - intervals": { "content": [ @@ -46,48 +46,48 @@ { "id": "test" }, - "test.bam:md5,096d269e17f4ae53f765013479240db8" + "test.bam:md5,51259943bca01c92b20fb5b7ac09a246" ] ], "1": [ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,096d269e17f4ae53f765013479240db8" + "test.bam:md5,51259943bca01c92b20fb5b7ac09a246" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:21:48.144461" + "timestamp": "2024-10-31T10:31:59.340916681" }, "sarscov2 - cram": { "content": [ [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:22:09.308602" + "timestamp": "2024-10-31T10:32:16.162569909" }, "test.cram": { "content": [ @@ -114,7 +114,7 @@ ] ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ @@ -128,15 +128,15 @@ ] ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:24:52.761169" + "timestamp": "2024-10-31T10:32:34.223186142" }, "sarscov2 - bam": { "content": [ @@ -146,35 +146,35 @@ { "id": "test" }, - "test.bam:md5,022271b9ce0a07579282a2a5c1186513" + "test.bam:md5,213acb451007a0098a6a6a360fa68d72" ] ], "1": [ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,022271b9ce0a07579282a2a5c1186513" + "test.bam:md5,213acb451007a0098a6a6a360fa68d72" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:21:28.719225" + "timestamp": "2024-10-31T10:31:44.601557038" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap index ad2fe8be65a..1f3e97cbfdc 100644 --- a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap @@ -22,14 +22,14 @@ "versions": { "content": [ [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T13:00:49.353138" + "timestamp": "2024-10-31T10:33:41.980566137" }, "human - vcf - stub": { "content": [ @@ -51,7 +51,7 @@ ] ], "2": [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ], "tbi": [ [ @@ -70,26 +70,26 @@ ] ], "versions": [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T13:01:24.370421" + "timestamp": "2024-10-31T10:34:08.561335315" }, "versions_allelspecific": { "content": [ [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T13:01:08.104194" + "timestamp": "2024-10-31T10:33:56.418381574" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap b/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap index cb2740864b2..afaec52efe4 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap +++ b/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,d567b20620f5adf0829cc4b4adb9f6ff" + "versions.yml:md5,64995de5e01e2d49fccd2b97df276d01" ], "csv": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,d567b20620f5adf0829cc4b4adb9f6ff" + "versions.yml:md5,64995de5e01e2d49fccd2b97df276d01" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-19T10:03:42.158801" + "timestamp": "2024-10-31T10:35:00.386844997" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap index 8291304ba87..c3fca758eb8 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:16:00.04396" + "timestamp": "2024-10-31T10:36:20.634357503" }, "sarscov2 - bam - intervals": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -55,15 +55,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:15:17.899391" + "timestamp": "2024-10-31T10:35:55.223087741" }, "sarscov2 - bam - multiple sites": { "content": [ @@ -77,7 +77,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -88,15 +88,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:15:47.770383" + "timestamp": "2024-10-31T10:36:10.08523788" }, "homo_sapiens - cram ": { "content": [ @@ -110,7 +110,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -121,15 +121,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:16:42.135898" + "timestamp": "2024-10-31T10:36:42.285370441" }, "sarscov2 - bam": { "content": [ @@ -143,7 +143,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -154,14 +154,14 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:14:57.629443" + "timestamp": "2024-10-31T10:35:41.89476551" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap index 48c322fd001..6936cf97175 100644 --- a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-19T14:20:12.168775" + "timestamp": "2024-10-31T10:37:25.720782902" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap index 5c2930f948f..756c2452f8a 100644 --- a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap @@ -2,38 +2,38 @@ "versions_pair": { "content": [ [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T11:08:17.057861" + "timestamp": "2024-10-31T10:39:04.844937172" }, "versions": { "content": [ [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T11:08:07.193762" + "timestamp": "2024-10-31T10:38:50.36175509" }, "versions_segmentation": { "content": [ [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T11:08:26.99069" + "timestamp": "2024-10-31T10:39:22.516513354" }, "segmentation": { "content": [ @@ -75,7 +75,7 @@ ] ], "2": [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ], "contamination": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:56:14.817045" + "timestamp": "2024-10-31T10:39:40.353818746" }, "human - pileup-table - matched-pair": { "content": [ diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap index d0d7b8b9dce..2ece2ae6151 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap @@ -9,14 +9,14 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:17.584362" + "timestamp": "2024-10-31T10:40:49.021126898" }, "test-gatk4-calibratedragstrmodel-cram": { "content": [ @@ -28,14 +28,14 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:30.21551" + "timestamp": "2024-10-31T10:41:19.764355383" }, "test-gatk4-calibratedragstrmodel-gzipped-beds": { "content": [ @@ -47,14 +47,14 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:53.619871" + "timestamp": "2024-10-31T10:42:13.527330586" }, "test-gatk4-calibratedragstrmodel-beds": { "content": [ @@ -66,13 +66,13 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:41.938548" + "timestamp": "2024-10-31T10:41:47.344014169" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap index 28a3a6e151b..212f950d28a 100644 --- a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap @@ -15,7 +15,7 @@ ] ], "2": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ], "hdf5": [ @@ -30,15 +30,15 @@ ] ], "versions": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:58:19.610687" + "timestamp": "2024-10-31T10:44:48.133712731" }, "test-gatk4-collectreadcounts-hdf5": { "content": [ @@ -69,7 +69,7 @@ ] ], "2": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ], "hdf5": [ @@ -84,14 +84,14 @@ ] ], "versions": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:58:07.500024" + "timestamp": "2024-10-31T10:44:24.624195466" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap index f35eb283db4..541e6c61216 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap @@ -20,13 +20,13 @@ ] ], [ - "versions.yml:md5,140780e1af7318cc9259b8970bc70c81" + "versions.yml:md5,2e89249bc2ef4e86a3fc59f0913c5525" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:34:12.568925" + "timestamp": "2024-10-31T10:45:25.930205969" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap index 7718ed00382..3be7acaa3ea 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap @@ -16,7 +16,7 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ], "interval_list": [ [ @@ -32,15 +32,15 @@ ] ], "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T21:26:22.252885" + "timestamp": "2024-10-31T10:37:46.848386632" }, "test_gatk4_intervallisttools -stub": { "content": [ @@ -59,7 +59,7 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ], "interval_list": [ [ @@ -75,14 +75,14 @@ ] ], "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:15:11.772344" + "timestamp": "2024-10-31T10:38:00.631338482" } } \ No newline at end of file From 4cc9150dc0edc6caf95dd29d24046b7591743ac3 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 31 Oct 2024 10:48:19 +0000 Subject: [PATCH 03/59] more tests --- .../collectsvevidence/tests/main.nf.test.snap | 44 +++++++++---------- .../combinegvcfs/tests/main.nf.test.snap | 18 ++++---- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap index 1f6992b8c64..cca8eea4c05 100644 --- a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap @@ -6,14 +6,14 @@ "chr22\t3320\t+\tchr22\t3482\t-\tnormal", "test.pe.txt.gz.tbi", [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:51:11.44656" + "timestamp": "2024-10-31T10:46:15.558451518" }, "test-gatk4-collectsvevidence-cram - stub": { "content": [ @@ -61,7 +61,7 @@ ], "6": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ], "paired_end_evidence": [ [ @@ -106,15 +106,15 @@ ] ], "versions": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:36:35.045647" + "timestamp": "2024-10-31T10:46:54.409850619" }, "test-gatk4-collectsvevidence-allele-count": { "content": [ @@ -125,14 +125,14 @@ "chr22\t1981\tnormal\t235\t0\t48\t0", "test.sd.txt.gz.tbi", [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:48:13.663238" + "timestamp": "2024-10-31T10:46:42.62581769" }, "test-gatk4-collectsvevidence-allele-count - stub": { "content": [ @@ -192,7 +192,7 @@ ] ], "6": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ], "paired_end_evidence": [ [ @@ -249,15 +249,15 @@ ] ], "versions": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:36:43.992644" + "timestamp": "2024-10-31T10:47:05.276032478" }, "test-gatk4-collectsvevidence-bam": { "content": [ @@ -266,13 +266,13 @@ "chr22\t3320\t+\tchr22\t3482\t-\tnormal", "test.pe.txt.gz.tbi", [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:51:22.087808" + "timestamp": "2024-10-31T10:46:29.443818792" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap index dfbd1ac1ef7..00aea2bdcca 100644 --- a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ], "combined_gvcf": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:35:25.18434" + "timestamp": "2024-10-31T10:47:56.847188152" }, "test_gatk4_combinegvcfs": { "content": [ @@ -169,13 +169,13 @@ "chr22\t4608\t.\tA\t\t.\t.\tEND=40001\tGT:DP:GQ:MIN_DP:PL\t./.:0:0:0:0,0,0" ], [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:41:25.316932" + "timestamp": "2024-10-31T10:47:45.34645647" } } \ No newline at end of file From 9ddb1a29183b6f56cc3709516d4154799b70f6dd Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 31 Oct 2024 12:12:04 +0000 Subject: [PATCH 04/59] more tests --- .../tests/main.nf.test.snap | 8 +- .../tests/main.nf.test.snap | 18 ++-- .../tests/main.nf.test.snap | 20 ++-- .../tests/main.nf.test.snap | 16 +-- .../gatk4/fastqtosam/tests/main.nf.test.snap | 26 ++--- .../filterintervals/tests/main.nf.test.snap | 10 +- .../filtermutectcalls/tests/main.nf.test.snap | 34 +++---- .../gatherbqsrreports/tests/main.nf.test.snap | 20 ++-- .../tests/main.nf.test.snap | 20 ++-- .../genomicsdbimport/tests/main.nf.test.snap | 34 +++---- .../genotypegvcfs/tests/main.nf.test.snap | 50 +++++----- .../tests/main.nf.test.snap | 38 +++---- .../haplotypecaller/tests/main.nf.test.snap | 32 +++--- .../indexfeaturefile/tests/main.nf.test.snap | 36 +++---- .../tests/main.nf.test.snap | 8 +- .../tests/main.nf.test.snap | 16 +-- .../mergebamalignment/tests/main.nf.test.snap | 18 ++-- .../mergemutectstats/tests/main.nf.test.snap | 18 ++-- .../gatk4/mutect2/tests/main.nf.test.snap | 56 +++++------ .../tests/main.nf.test.snap | 10 +- .../gatk4/printreads/tests/main.nf.test.snap | 18 ++-- .../gatk4/reblockgvcf/tests/main.nf.test.snap | 24 ++--- .../gatk4/revertsam/tests/main.nf.test.snap | 18 ++-- .../gatk4/samtofastq/tests/main.nf.test.snap | 24 ++--- .../gatk4/shiftfasta/tests/main.nf.test.snap | 10 +- .../gatk4/splitcram/tests/main.nf.test.snap | 18 ++-- .../splitintervals/tests/main.nf.test.snap | 30 +++--- .../splitncigarreads/tests/main.nf.test.snap | 16 +-- .../gatk4/svannotate/tests/main.nf.test.snap | 24 ++--- .../gatk4/svcluster/tests/main.nf.test.snap | 8 +- .../variantfiltration/tests/main.nf.test.snap | 16 +-- .../variantstotable/tests/main.nf.test.snap | 99 +++++++++---------- 32 files changed, 396 insertions(+), 397 deletions(-) diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap index 02136a8b365..4a62f028b5d 100644 --- a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "genome.zip", [ - "versions.yml:md5,755f9a44a99148151b624d70eb6ce260" + "versions.yml:md5,b70639968daefca28136a26156170e29" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:37:10.366333" + "timestamp": "2024-10-31T10:48:46.420056406" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap index b9dddfbb989..ac0a8fa58fd 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + "versions.yml:md5,f1e49a983c12aa65895e70405a9dfc14" ], "condensed_evidence": [ [ @@ -42,15 +42,15 @@ ] ], "versions": [ - "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + "versions.yml:md5,f1e49a983c12aa65895e70405a9dfc14" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:42:07.848497" + "timestamp": "2024-10-31T10:49:51.212441436" }, "test-gatk4-condensdepthevidence": { "content": [ @@ -60,13 +60,13 @@ ], "test.rd.txt.gz.tbi", [ - "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + "versions.yml:md5,f1e49a983c12aa65895e70405a9dfc14" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:33:21.910858" + "timestamp": "2024-10-31T10:49:37.340222412" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap index 16735f9549a..e8a600fd114 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ], "dict": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:16:16.34453" + "timestamp": "2024-10-31T10:51:56.155954077" }, "sarscov2 - fasta": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ], "dict": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T13:58:25.822068" + "timestamp": "2024-10-31T10:51:45.562993875" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap index bbcef1471e0..fa478ca8f7a 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "test.metrics", [ - "versions.yml:md5,1d9c175d88b6c50c7dc999c1f70261a8" + "versions.yml:md5,a7b6a9d538151a577da5f5727ace31e6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T14:41:39.857566" + "timestamp": "2024-10-31T11:01:20.304274717" }, "sarscov2 - bam - stub": { "content": [ @@ -29,13 +29,13 @@ "content": [ "test.metrics", [ - "versions.yml:md5,1d9c175d88b6c50c7dc999c1f70261a8" + "versions.yml:md5,a7b6a9d538151a577da5f5727ace31e6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T14:24:41.460191" + "timestamp": "2024-10-31T11:00:54.378191881" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap index a4b44520dc5..5c575866db7 100644 --- a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ], "bam": [ [ @@ -24,40 +24,40 @@ ] ], "versions": [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:43:37.316141" + "timestamp": "2024-10-31T11:02:58.024964061" }, "test-gatk4-fastqtosam-single-end": { "content": [ "e6a4aa204d980e177a0458596f0a70ac", [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:29:12.362942" + "timestamp": "2024-10-31T11:02:34.422399439" }, "test-gatk4-fastqtosam-paired-end": { "content": [ "e6a4aa204d980e177a0458596f0a70ac", [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:29:22.385798" + "timestamp": "2024-10-31T11:02:47.309600742" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap index c9626666948..add6095b313 100644 --- a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30" + "versions.yml:md5,6fbacd816f4d48eae20f1fd423cb4e56" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30" + "versions.yml:md5,6fbacd816f4d48eae20f1fd423cb4e56" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:25:35.933532" + "timestamp": "2024-10-31T11:03:52.645895175" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap index 1c39e3b5d7c..28a63357e7f 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap @@ -12,14 +12,14 @@ "versions_with-files": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:45:43.679571" + "timestamp": "2024-10-31T11:04:55.625468064" }, "human - vcf - stub": { "content": [ @@ -49,7 +49,7 @@ ] ], "3": [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ], "stats": [ [ @@ -76,39 +76,39 @@ ] ], "versions": [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:46:32.666273" + "timestamp": "2024-10-31T11:05:33.111919824" }, "versions_use-val": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:46:03.876073" + "timestamp": "2024-10-31T11:05:19.277193087" }, "versions_base": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:47:39.930795" + "timestamp": "2024-10-31T11:04:36.657284567" }, "human - vcf - with-files": { "content": [ diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap index bc5d4bd1332..e792d07ec56 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ], "table": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:22:34.490694" + "timestamp": "2024-10-31T11:07:33.025431761" }, "test-gatk4-gatherbqsrreports": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ], "table": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:22:10.552951" + "timestamp": "2024-10-31T11:07:09.791064374" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap index fd9f2583440..e7094d73f4b 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ], "table": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:44:42.759098" + "timestamp": "2024-10-31T11:08:38.118444526" }, "test-gatk4-gatherpileupsummaries": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ], "table": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:18:40.835226" + "timestamp": "2024-10-31T11:08:17.759423015" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap index 55ced0d8802..cb47a432c9e 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "test.interval_list:md5,4c85812ac15fc1cd29711a851d23c0bf", [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:42:51.836379" + "timestamp": "2024-10-31T11:09:55.9195126" }, "test_gatk4_genomicsdbimport_create_genomicsdb": { "content": [ @@ -22,14 +22,14 @@ "vidmap.json" ], [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:42:36.846239" + "timestamp": "2024-10-31T11:09:25.302350893" }, "test_gatk4_genomicsdbimport_update_genomicsdb": { "content": [ @@ -41,14 +41,14 @@ "vidmap.json" ], [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:43:09.00769" + "timestamp": "2024-10-31T11:10:13.206208761" }, "test_gatk4_genomicsdbimport_stub": { "content": [ @@ -68,7 +68,7 @@ ], "3": [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ], "genomicsdb": [ [ @@ -85,14 +85,14 @@ ], "versions": [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:43:20.921712" + "timestamp": "2024-10-31T11:10:36.510210505" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap index 1621618e7a9..30e2dc1cc6a 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap @@ -18,14 +18,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:27:24.926097884" + "timestamp": "2024-10-31T11:16:45.625453031" }, "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []": { "content": [ @@ -46,14 +46,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:26:24.426228557" + "timestamp": "2024-10-31T11:15:55.296562046" }, "homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []": { "content": [ @@ -74,14 +74,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:27:04.179308513" + "timestamp": "2024-10-31T11:16:30.471742609" }, "homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi": { "content": [ @@ -102,14 +102,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:26:43.9088684" + "timestamp": "2024-10-31T11:16:13.266019505" }, "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub": { "content": [ @@ -131,7 +131,7 @@ ] ], "2": [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ], "tbi": [ [ @@ -150,15 +150,15 @@ ] ], "versions": [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:19:57.615552867" + "timestamp": "2024-10-31T11:17:19.342242664" }, "homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []": { "content": [ @@ -179,13 +179,13 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:27:46.189794941" + "timestamp": "2024-10-31T11:17:01.475664058" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap index d9304bcdc5c..e44c13bad89 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ], "table": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:18:25.186463" + "timestamp": "2024-10-31T11:19:28.038865911" }, "human - bam": { "content": [ @@ -40,30 +40,30 @@ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "1": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ], "table": [ [ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "versions": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T14:14:59.7414" + "timestamp": "2024-10-31T11:18:47.633313304" }, "human - cram": { "content": [ @@ -73,29 +73,29 @@ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "1": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ], "table": [ [ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "versions": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T14:15:25.680928" + "timestamp": "2024-10-31T11:19:14.207172594" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap index 0203fcfcf48..e3ba2bdfa96 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap @@ -4,55 +4,55 @@ "test_cram.vcf.gz", "test_cram.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:36:54.158605" + "timestamp": "2024-10-31T11:20:32.392608448" }, "homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi": { "content": [ "test_cram_sites.vcf.gz", "test_cram_sites.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:37:13.77024" + "timestamp": "2024-10-31T11:20:49.012555768" }, "homo_sapiens - [bam, bai] - fasta - fai - dict": { "content": [ "test_bam.vcf.gz", "test_bam.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:36:34.77631" + "timestamp": "2024-10-31T11:20:09.342159899" }, "homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi": { "content": [ "test_cram_sites_dragstr.vcf.gz", "test_cram_sites_dragstr.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:37:32.967085" + "timestamp": "2024-10-31T11:21:06.551678783" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap index fc19333634f..788b9290b87 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap @@ -12,14 +12,14 @@ "test_gatk4_indexfeaturefile_vcf": { "content": [ [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:20.602472" + "timestamp": "2024-10-31T11:22:21.619530121" }, "geneome.bed.idx": { "content": [ @@ -53,7 +53,7 @@ ] ], "1": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ], "index": [ [ @@ -64,15 +64,15 @@ ] ], "versions": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:03.058351" + "timestamp": "2024-10-31T11:22:06.537858152" }, "test_gatk4_indexfeaturefile_vcf_gz": { "content": [ @@ -86,7 +86,7 @@ ] ], "1": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ], "index": [ [ @@ -97,15 +97,15 @@ ] ], "versions": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:51.861697" + "timestamp": "2024-10-31T11:22:37.41693965" }, "test.genome.vcf.idx": { "content": [ @@ -120,13 +120,13 @@ "test_gatk4_indexfeaturefile_bed": { "content": [ [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:56:46.885162" + "timestamp": "2024-10-31T11:21:52.805375486" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap index b829bd9c4aa..638e058359c 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap @@ -9,13 +9,13 @@ "CAA\tTTG\t0.0\t3.4445551925564533E-6\t3.435193155024585E-6\t5.139879646597498E-6\t0.0\t3.4674461103560476E-6\t3.428570449688764E-6\t6.343168047383713E-6\t0.9945238954147358\t1.3629167993931722E-4\t0.0052793454402581125\t3.5208652465150646E-5\t29263\t197" ], [ - "versions.yml:md5,88928ff140a0967e574e66944fd2a2f2" + "versions.yml:md5,e8e087001bd49c02f325e90b1fbeb44d" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:16:08.296564" + "timestamp": "2024-10-31T11:24:53.596350009" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap index f500c0dcc08..e28a7be77b0 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap @@ -4,27 +4,27 @@ "85745045e9c55d3846d80bfde08a7d34", "test.normalised.vcf.gz.tbi", [ - "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61" + "versions.yml:md5,b8e7f53a1e802cf29ff86c9d1aaae5da" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:09:35.03744" + "timestamp": "2024-10-31T11:25:49.57287314" }, "test-gatk4-leftalignandtrimvariants-interval": { "content": [ "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]", "test.normalised.vcf.gz.tbi", [ - "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61" + "versions.yml:md5,b8e7f53a1e802cf29ff86c9d1aaae5da" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:11:42.893725" + "timestamp": "2024-10-31T11:25:35.479943622" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap index 719a7bb3311..476eecdfd08 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions.yml:md5,19f0b1268d925943a61f6f686061d519" ], "bam": [ [ @@ -22,27 +22,27 @@ ] ], "versions": [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions.yml:md5,19f0b1268d925943a61f6f686061d519" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:02:15.41024" + "timestamp": "2024-10-31T11:29:07.319519362" }, "test-gatk4-mergebamalignment": { "content": [ "30c325e1e032eb1782a280d34c0fb1c7", [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions.yml:md5,19f0b1268d925943a61f6f686061d519" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:02:08.379035" + "timestamp": "2024-10-31T11:28:55.287907787" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap index d0279f272e4..77da5d78203 100644 --- a/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,7298d6e6e18024f7c2ed0fe38d259a52" + "versions.yml:md5,2b6e8361dd6734be029e7480dbcb7794" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:13:56.2195" + "timestamp": "2024-10-31T11:29:44.84165293" }, "human - stats,tsv - stub": { "content": [ @@ -24,7 +24,7 @@ ] ], "1": [ - "versions.yml:md5,7298d6e6e18024f7c2ed0fe38d259a52" + "versions.yml:md5,2b6e8361dd6734be029e7480dbcb7794" ], "stats": [ [ @@ -36,15 +36,15 @@ ] ], "versions": [ - "versions.yml:md5,7298d6e6e18024f7c2ed0fe38d259a52" + "versions.yml:md5,2b6e8361dd6734be029e7480dbcb7794" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:14:10.058769" + "timestamp": "2024-10-31T11:29:54.48600467" }, "human - stats, tsv": { "content": [ diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap index f047af19dd9..b37450f4f47 100644 --- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap @@ -14,14 +14,14 @@ "test.f1r2.tar.gz" ], [ - "h" + "w" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-21T10:14:45.599103891" + "timestamp": "2024-10-31T11:49:16.64829295" }, "generate_pon": { "content": [ @@ -43,14 +43,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:57:18.264453766" + "timestamp": "2024-10-31T11:48:44.796786166" }, "mitochondria": { "content": [ @@ -72,14 +72,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T16:05:47.668766905" + "timestamp": "2024-10-31T11:49:03.399442766" }, "cram_input": { "content": [ @@ -101,14 +101,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:52:27.894730554" + "timestamp": "2024-10-31T11:45:49.212101867" }, "tumor_single": { "content": [ @@ -130,14 +130,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:43:28.935723443" + "timestamp": "2024-10-31T11:42:47.335589964" }, "tumor_normal_pair": { "content": [ @@ -161,14 +161,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:31:31.913366311" + "timestamp": "2024-10-31T11:36:10.506528759" }, "tumor_normal_pair_f1r2": { "content": [ @@ -192,13 +192,13 @@ "test.f1r2.tar.gz" ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-21T09:45:52.321385704" + "timestamp": "2024-10-31T11:39:21.909639821" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap index 5365291dab8..127164975e3 100644 --- a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4" + "versions.yml:md5,275510c640bbc3050a257bece1e51f85" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4" + "versions.yml:md5,275510c640bbc3050a257bece1e51f85" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:58:51.314382" + "timestamp": "2024-10-31T11:55:38.222687003" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap index 7f1266f2641..b847f44a910 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap @@ -9,32 +9,32 @@ ], [ - "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" + "versions.yml:md5,b14bcdd8d9bfcf5b7e8f1f58b79fd179" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:48:53.871683" + "timestamp": "2024-10-31T11:56:25.490158526" }, "test-gatk4-printreads-cram": { "content": [ [ ], - "591299d00e262474250c5ccc241bba59", + "d105c4aee01f68ada72b288b1fd72f35", [ ], [ - "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" + "versions.yml:md5,b14bcdd8d9bfcf5b7e8f1f58b79fd179" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:42:29.968056" + "timestamp": "2024-10-31T11:56:39.698048025" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap index 6121c3d208a..df58a6495e8 100644 --- a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap @@ -4,41 +4,41 @@ "test.rb.g.vcf.gz", "test.rb.g.vcf.gz.tbi", [ - "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + "versions.yml:md5,29d0014d4e4858fac9d984ed0d6d7dd2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:32:19.353113" + "timestamp": "2024-10-31T11:58:15.459756351" }, "test_gatk4_reblockgvcf_intervals": { "content": [ "test.rb.g.vcf.gz", "test.rb.g.vcf.gz.tbi", [ - "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + "versions.yml:md5,29d0014d4e4858fac9d984ed0d6d7dd2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:32:11.896391" + "timestamp": "2024-10-31T11:58:04.712624842" }, "test_gatk4_reblockgvcf": { "content": [ "test.rb.g.vcf.gz", "test.rb.g.vcf.gz.tbi", [ - "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + "versions.yml:md5,29d0014d4e4858fac9d984ed0d6d7dd2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:32:00.687676" + "timestamp": "2024-10-31T11:57:51.607837498" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap index 1cbb5ce6e79..72fda7af8e4 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "e3cfa46b13cc4fc425cccae944f43b10", [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions.yml:md5,ef0c48b3a3499410f2ed092a3e9814b4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:45:39.712635" + "timestamp": "2024-10-31T11:58:52.167057245" }, "test-gatk4-revertsam-stubs": { "content": [ @@ -24,7 +24,7 @@ ] ], "1": [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions.yml:md5,ef0c48b3a3499410f2ed092a3e9814b4" ], "bam": [ [ @@ -35,14 +35,14 @@ ] ], "versions": [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions.yml:md5,ef0c48b3a3499410f2ed092a3e9814b4" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:45:46.856318" + "timestamp": "2024-10-31T11:59:02.762117999" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap index 0e1ec4b79d4..38040db0ee4 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap @@ -9,14 +9,14 @@ "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE Date: Mon, 4 Nov 2024 09:31:29 +0000 Subject: [PATCH 05/59] linting --- modules/nf-core/gatk4/splitintervals/meta.yml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/gatk4/splitintervals/meta.yml b/modules/nf-core/gatk4/splitintervals/meta.yml index 6a1b869b0d1..62dc03b0e8c 100644 --- a/modules/nf-core/gatk4/splitintervals/meta.yml +++ b/modules/nf-core/gatk4/splitintervals/meta.yml @@ -57,9 +57,18 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test' ] + pattern: "*.interval_list" - "**.interval_list": - type: file - description: interval files + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + pattern: "*.interval_list" + - s: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] pattern: "*.interval_list" - versions: - versions.yml: From 79b7604d0f04ec9fdd4812b78065b124d3635826 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 4 Nov 2024 09:43:02 +0000 Subject: [PATCH 06/59] linting --- modules/nf-core/gatk4/collectsvevidence/meta.yml | 4 ++-- modules/nf-core/gatk4/printsvevidence/meta.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/gatk4/collectsvevidence/meta.yml b/modules/nf-core/gatk4/collectsvevidence/meta.yml index a9d64d30e50..5ee2b975c7f 100644 --- a/modules/nf-core/gatk4/collectsvevidence/meta.yml +++ b/modules/nf-core/gatk4/collectsvevidence/meta.yml @@ -37,8 +37,8 @@ input: pattern: "*.vcf.gz" - site_depth_vcf_tbi: type: file - description: Optional - input VCF TBI of SNPs marking loci for site depths, needed - for the site depths output + description: Optional - input VCF TBI of SNPs marking loci for site depths, + needed for the site depths output pattern: "*.vcf.gz.tbi" - - fasta: type: file diff --git a/modules/nf-core/gatk4/printsvevidence/meta.yml b/modules/nf-core/gatk4/printsvevidence/meta.yml index 3e3ad72d58e..07ea1223fd0 100644 --- a/modules/nf-core/gatk4/printsvevidence/meta.yml +++ b/modules/nf-core/gatk4/printsvevidence/meta.yml @@ -70,8 +70,8 @@ output: e.g. [ id:'test', single_end:false ] - "*.txt.gz.tbi": type: file - description: The index file of the output compressed text file containing the discordant read - pairs or the soft clipped reads + description: The index file of the output compressed text file containing the + discordant read pairs or the soft clipped reads pattern: "*.{pe,sr,baf,rd}.txt.gz.tbi" - versions: - versions.yml: From 6cea208be075ed7c6d8ff3338224b41e0b687d4c Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 4 Nov 2024 11:49:09 +0000 Subject: [PATCH 07/59] migrate gatk4/createsomaticpanelofnormals to nf-test --- .../gatk4/createsomaticpanelofnormals/main.nf | 15 +++ .../tests/main.nf.test | 82 ++++++++++++++ .../tests/main.nf.test.snap | 100 ++++++++++++++++++ tests/config/pytest_modules.yml | 6 -- .../gatk4/createsomaticpanelofnormals/main.nf | 27 ----- .../nextflow.config | 13 --- .../createsomaticpanelofnormals/test.yml | 10 -- 7 files changed, 197 insertions(+), 56 deletions(-) create mode 100644 modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf delete mode 100644 tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index ffd77888ed0..b35412dce68 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -45,4 +45,19 @@ process GATK4_CREATESOMATICPANELOFNORMALS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "${prefix}" | gzip -c > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + + } diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test new file mode 100644 index 00000000000..d602b9c7688 --- /dev/null +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test @@ -0,0 +1,82 @@ +nextflow_process { + + name "Test Process GATK4_CREATESOMATICPANELOFNORMALS" + script "../main.nf" + process "GATK4_CREATESOMATICPANELOFNORMALS" + + tag "modules" + tag "modules_nfcore" + tag "untar" + tag "gatk4" + tag "gatk4/createsomaticpanelofnormals" + + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [[id:'test'], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ] + """ + } + } + } + + test("homo sapiens - genomicsdb") { + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = [ [ id:'genome' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - genomicsdb - stub") { + + options "-stub" + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = [ [ id:'genome' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap new file mode 100644 index 00000000000..098b9852fe6 --- /dev/null +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap @@ -0,0 +1,100 @@ +{ + "homo sapiens - genomicsdb": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,bd443afef3ba3aa5b7f5652313664e9e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4" + ] + ], + "2": [ + "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,bd443afef3ba3aa5b7f5652313664e9e" + ] + ], + "versions": [ + "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T11:37:41.734498184" + }, + "homo sapiens - genomicsdb - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" + ] + ], + "versions": [ + "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T11:37:55.969655125" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 832f747e594..e228149373b 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -200,12 +200,6 @@ gatk/indelrealigner: gatk4/cnnscorevariants: - modules/nf-core/gatk4/cnnscorevariants/** - tests/modules/nf-core/gatk4/cnnscorevariants/** -gatk4/createreadcountpanelofnormals: - - modules/nf-core/gatk4/createreadcountpanelofnormals/** - - tests/modules/nf-core/gatk4/createreadcountpanelofnormals/** -gatk4/createsomaticpanelofnormals: - - modules/nf-core/gatk4/createsomaticpanelofnormals/** - - tests/modules/nf-core/gatk4/createsomaticpanelofnormals/** gatk4/determinegermlinecontigploidy: - modules/nf-core/gatk4/determinegermlinecontigploidy/** - tests/modules/nf-core/gatk4/determinegermlinecontigploidy/** diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf deleted file mode 100644 index bd626961f69..00000000000 --- a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' -include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../../modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf' - -workflow test_gatk4_createsomaticpanelofnormals { - db = [[], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ] - - UNTAR ( db ) - - input = Channel.of([ id:'test']) - .combine(UNTAR.out.untar.map{ it[1] }) - - fasta = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - fai = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - dict = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - ] - - GATK4_CREATESOMATICPANELOFNORMALS ( input, fasta, fai, dict ) -} diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config deleted file mode 100644 index 0db1ebba6c2..00000000000 --- a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config +++ /dev/null @@ -1,13 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GATK4_CREATESOMATICPANELOFNORMALS { - ext.prefix = { "${meta.id}.pon" } - } - - withName: UNTAR { - publishDir = [ enabled: false ] - } - -} diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml deleted file mode 100644 index a2a9fc182ae..00000000000 --- a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: gatk4 createsomaticpanelofnormals test_gatk4_createsomaticpanelofnormals - command: nextflow run ./tests/modules/nf-core/gatk4/createsomaticpanelofnormals -entry test_gatk4_createsomaticpanelofnormals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config - tags: - - gatk4/createsomaticpanelofnormals - - gatk4 - files: - - path: output/gatk4/test.pon.vcf.gz - - path: output/gatk4/test.pon.vcf.gz.tbi - md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 - - path: output/gatk4/versions.yml From 93891beb649d8fceeee0538b8e9535364692eb71 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 4 Nov 2024 13:40:50 +0000 Subject: [PATCH 08/59] migrate printsvevidence --- modules/nf-core/gatk4/printsvevidence/main.nf | 12 ++ .../gatk4/printsvevidence/tests/main.nf.test | 109 +++++++++++++++ .../printsvevidence/tests/main.nf.test.snap | 129 ++++++++++++++++++ .../printsvevidence/tests/nextflow.config | 5 + tests/config/pytest_modules.yml | 3 - .../nf-core/gatk4/printsvevidence/main.nf | 106 -------------- .../gatk4/printsvevidence/nextflow.config | 9 -- .../nf-core/gatk4/printsvevidence/test.yml | 55 -------- 8 files changed, 255 insertions(+), 173 deletions(-) create mode 100644 modules/nf-core/gatk4/printsvevidence/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/printsvevidence/tests/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/printsvevidence/main.nf delete mode 100644 tests/modules/nf-core/gatk4/printsvevidence/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/printsvevidence/test.yml diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index c4e42bbc5eb..a303b535714 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -63,4 +63,16 @@ process GATK4_PRINTSVEVIDENCE { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip -c > printed_evidence.txt.gz + touch printed_evidence.txt.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test new file mode 100644 index 00000000000..341989aca52 --- /dev/null +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test @@ -0,0 +1,109 @@ +nextflow_process { + + name "Test Process GATK4_PRINTSVEVIDENCE" + script "../main.nf" + config "./nextflow.config" + process "GATK4_PRINTSVEVIDENCE" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectsvevidence" + tag "gatk4/printsvevidence" + + setup { + run("GATK4_COLLECTSVEVIDENCE") { + script "../../collectsvevidence/main.nf" + process { + """ + input[0] = Channel.of( + [ + [ id:'normal' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [], + [] + ], + [ + [ id:'tumor' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + [], + [] + ] + ) + input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + } + + test("homo sapiens - bam") { + + when { + process { + """ + files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence + indices = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index + input_svevidence = files + .combine(indices, by:0) + .map({ meta, file, index -> + [[], file, index ] + }) + .groupTuple() + + input[0] = input_svevidence + input[1] = [] + input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[4] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence + indices = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index + input_svevidence = files + .combine(indices, by:0) + .map({ meta, file, index -> + [[], file, index ] + }) + .groupTuple() + + input[0] = input_svevidence + input[1] = [] + input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[4] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap new file mode 100644 index 00000000000..aff2e29ad80 --- /dev/null +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap @@ -0,0 +1,129 @@ +{ + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + + ], + "printed_evidence": [ + + ], + "printed_evidence_index": [ + + ], + "versions": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T13:26:54.025037485" + }, + "homo sapiens - bam": { + "content": [ + { + "0": [ + [ + [ + + ], + "[].pe.txt.gz:md5,e466bbd14a1e511f296f8943ec60ca61" + ] + ], + "1": [ + [ + [ + + ], + "[].pe.txt.gz.tbi:md5,e56c7481a5f4ff1a14079d9d2bb12a2d" + ] + ], + "2": [ + "versions.yml:md5,ed39ded39eeae49d2aac81c45fb17c26" + ], + "printed_evidence": [ + [ + [ + + ], + "[].pe.txt.gz:md5,e466bbd14a1e511f296f8943ec60ca61" + ] + ], + "printed_evidence_index": [ + [ + [ + + ], + "[].pe.txt.gz.tbi:md5,e56c7481a5f4ff1a14079d9d2bb12a2d" + ] + ], + "versions": [ + "versions.yml:md5,ed39ded39eeae49d2aac81c45fb17c26" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T13:26:38.860459499" + }, + "homo sapiens - bam - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + "printed_evidence.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + [ + + ], + "printed_evidence.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,ed39ded39eeae49d2aac81c45fb17c26" + ], + "printed_evidence": [ + [ + [ + + ], + "printed_evidence.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "printed_evidence_index": [ + [ + [ + + ], + "printed_evidence.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ed39ded39eeae49d2aac81c45fb17c26" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T13:40:15.747273218" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/printsvevidence/tests/nextflow.config b/modules/nf-core/gatk4/printsvevidence/tests/nextflow.config new file mode 100644 index 00000000000..1d90e59c76e --- /dev/null +++ b/modules/nf-core/gatk4/printsvevidence/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GATK4_COLLECTSVEVIDENCE { + ext.args = {"--sample-name ${meta.id}"} + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index e228149373b..8e0512a5132 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -215,9 +215,6 @@ gatk4/intervallisttobed: gatk4/postprocessgermlinecnvcalls: - modules/nf-core/gatk4/postprocessgermlinecnvcalls/** - tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/** -gatk4/printsvevidence: - - modules/nf-core/gatk4/printsvevidence/** - - tests/modules/nf-core/gatk4/printsvevidence/** gatk4/selectsamples: - modules/nf-core/gatk4/selectsamples/** - tests/modules/nf-core/gatk4/selectsamples/** diff --git a/tests/modules/nf-core/gatk4/printsvevidence/main.nf b/tests/modules/nf-core/gatk4/printsvevidence/main.nf deleted file mode 100644 index 16309838a94..00000000000 --- a/tests/modules/nf-core/gatk4/printsvevidence/main.nf +++ /dev/null @@ -1,106 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_PRINTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/printsvevidence/main.nf' -include { GATK4_COLLECTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' - -workflow test_gatk4_printsvevidence { - - input = Channel.of( - [ - [ id:'normal' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - [], - [] - ], - [ - [ id:'tumor' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - [], - [] - ] - ) - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - - GATK4_COLLECTSVEVIDENCE( - input, - fasta, - fasta_fai, - dict - ) - - files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence - - indices = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index - - input_svevidence = files.combine(indices, by:0).map({ meta, file, index -> - [ [id:'pe_files'], file, index ] - }) - .groupTuple() - - GATK4_PRINTSVEVIDENCE( - input_svevidence, - [], - fasta, - fasta_fai, - dict - ) -} - -workflow test_gatk4_printsvevidence_bed_no_fasta { - - input = Channel.of( - [ - [ id:'normal', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - [], - [] - ], - [ - [ id:'tumor', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - [], - [] - ] - ) - - fasta = [] - fasta_fai = [] - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) - - GATK4_COLLECTSVEVIDENCE( - input, - fasta, - fasta_fai, - dict - ) - - files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence - - indices = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index - - input_svevidence = files.combine(indices, by:0).map({ meta, file, index -> - [ [id:'pe_files'], file, index ] - }) - .groupTuple() - - GATK4_PRINTSVEVIDENCE( - input_svevidence, - [], - fasta, - fasta_fai, - dict - ) - -} diff --git a/tests/modules/nf-core/gatk4/printsvevidence/nextflow.config b/tests/modules/nf-core/gatk4/printsvevidence/nextflow.config deleted file mode 100644 index 54136c7018b..00000000000 --- a/tests/modules/nf-core/gatk4/printsvevidence/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GATK4_COLLECTSVEVIDENCE { - ext.args = {"--sample-name ${meta.id}"} - } - -} diff --git a/tests/modules/nf-core/gatk4/printsvevidence/test.yml b/tests/modules/nf-core/gatk4/printsvevidence/test.yml deleted file mode 100644 index 26f16234a97..00000000000 --- a/tests/modules/nf-core/gatk4/printsvevidence/test.yml +++ /dev/null @@ -1,55 +0,0 @@ -- name: gatk4 printsvevidence test_gatk4_printsvevidence - command: nextflow run ./tests/modules/nf-core/gatk4/printsvevidence -entry test_gatk4_printsvevidence -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printsvevidence/nextflow.config - tags: - - gatk4/printsvevidence - - gatk4 - files: - - path: output/gatk4/normal.pe.txt.gz - md5sum: 19f13dd0408204590b40239d14acbdde - - path: output/gatk4/normal.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/normal.sr.txt.gz - md5sum: fb9ce52193a0db3a084890bd6bbf6a64 - - path: output/gatk4/normal.sr.txt.gz.tbi - md5sum: 33b3a9ff444eb0e0fc3016239651f05f - - path: output/gatk4/pe_files.pe.txt.gz - md5sum: 01af37919a5df7353096789fe526a33f - - path: output/gatk4/pe_files.pe.txt.gz.tbi - md5sum: e56c7481a5f4ff1a14079d9d2bb12a2d - - path: output/gatk4/tumor.pe.txt.gz - md5sum: 45be73eb7d52e901b6dd8a5e48bf2161 - - path: output/gatk4/tumor.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/tumor.sr.txt.gz - md5sum: afdf79e9b07035df28d6c8313661931b - - path: output/gatk4/tumor.sr.txt.gz.tbi - md5sum: 8207e46090fdbe125ce6936ac383da40 - - path: output/gatk4/versions.yml - -- name: gatk4 printsvevidence test_gatk4_printsvevidence_bed_no_fasta - command: nextflow run ./tests/modules/nf-core/gatk4/printsvevidence -entry test_gatk4_printsvevidence_bed_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printsvevidence/nextflow.config - tags: - - gatk4/printsvevidence - - gatk4 - files: - - path: output/gatk4/normal.pe.txt.gz - md5sum: 19f13dd0408204590b40239d14acbdde - - path: output/gatk4/normal.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/normal.sr.txt.gz - md5sum: fb9ce52193a0db3a084890bd6bbf6a64 - - path: output/gatk4/normal.sr.txt.gz.tbi - md5sum: 33b3a9ff444eb0e0fc3016239651f05f - - path: output/gatk4/pe_files.pe.txt.gz - md5sum: 01af37919a5df7353096789fe526a33f - - path: output/gatk4/pe_files.pe.txt.gz.tbi - md5sum: e56c7481a5f4ff1a14079d9d2bb12a2d - - path: output/gatk4/tumor.pe.txt.gz - md5sum: 45be73eb7d52e901b6dd8a5e48bf2161 - - path: output/gatk4/tumor.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/tumor.sr.txt.gz - md5sum: afdf79e9b07035df28d6c8313661931b - - path: output/gatk4/tumor.sr.txt.gz.tbi - md5sum: 8207e46090fdbe125ce6936ac383da40 - - path: output/gatk4/versions.yml From 85cd93b06ba493cae79a8c42858a71bd97c8b895 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 4 Nov 2024 13:46:14 +0000 Subject: [PATCH 09/59] migrate intervallisttobed --- .../nf-core/gatk4/intervallisttobed/main.nf | 12 ++++ .../intervallisttobed/tests/main.nf.test | 58 +++++++++++++++ .../intervallisttobed/tests/main.nf.test.snap | 72 +++++++++++++++++++ tests/config/pytest_modules.yml | 3 - .../nf-core/gatk4/intervallisttobed/main.nf | 15 ---- .../gatk4/intervallisttobed/nextflow.config | 5 -- .../nf-core/gatk4/intervallisttobed/test.yml | 9 --- 7 files changed, 142 insertions(+), 32 deletions(-) create mode 100644 modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/gatk4/intervallisttobed/main.nf delete mode 100644 tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/intervallisttobed/test.yml diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 61f68a68dcf..dafcccda5c4 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -40,4 +40,16 @@ process GATK4_INTERVALLISTTOBED { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test new file mode 100644 index 00000000000..e801b06654d --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test @@ -0,0 +1,58 @@ +nextflow_process { + + name "Test Process GATK4_INTERVALLISTTOBED" + script "../main.nf" + process "GATK4_INTERVALLISTTOBED" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/intervallisttobed" + + test("homo sapiens - bed") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - bed - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test.snap new file mode 100644 index 00000000000..0664f5e913f --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "homo sapiens - bed": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,9046675d01199fbbee79f2bc1c5dce52" + ] + ], + "1": [ + "versions.yml:md5,27876d5035fa3f6d4750152ed4033259" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,9046675d01199fbbee79f2bc1c5dce52" + ] + ], + "versions": [ + "versions.yml:md5,27876d5035fa3f6d4750152ed4033259" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T13:44:42.715318379" + }, + "homo sapiens - bed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,27876d5035fa3f6d4750152ed4033259" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,27876d5035fa3f6d4750152ed4033259" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T13:45:01.440631153" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 8e0512a5132..0d111be9b62 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -209,9 +209,6 @@ gatk4/filtervarianttranches: gatk4/germlinecnvcaller: - modules/nf-core/gatk4/germlinecnvcaller/** - tests/modules/nf-core/gatk4/germlinecnvcaller/** -gatk4/intervallisttobed: - - modules/nf-core/gatk4/intervallisttobed/** - - tests/modules/nf-core/gatk4/intervallisttobed/** gatk4/postprocessgermlinecnvcalls: - modules/nf-core/gatk4/postprocessgermlinecnvcalls/** - tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/** diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/main.nf b/tests/modules/nf-core/gatk4/intervallisttobed/main.nf deleted file mode 100644 index c8a5b819098..00000000000 --- a/tests/modules/nf-core/gatk4/intervallisttobed/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_INTERVALLISTTOBED } from '../../../../../modules/nf-core/gatk4/intervallisttobed/main.nf' - -workflow test_gatk4_intervallisttobed { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) - ] - - GATK4_INTERVALLISTTOBED ( input ) -} diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config b/tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/test.yml b/tests/modules/nf-core/gatk4/intervallisttobed/test.yml deleted file mode 100644 index 461d484c855..00000000000 --- a/tests/modules/nf-core/gatk4/intervallisttobed/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: gatk4 intervallisttobed - command: nextflow run ./tests/modules/nf-core/gatk4/intervallisttobed -entry test_gatk4_intervallisttobed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config - tags: - - gatk4 - - gatk4/intervallisttobed - files: - - path: output/gatk4/test.bed - md5sum: 9046675d01199fbbee79f2bc1c5dce52 - - path: output/gatk4/versions.yml From 523fe160d4fc39928a4b0d7124a26f5403edfb83 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 4 Nov 2024 14:45:52 +0000 Subject: [PATCH 10/59] migrate filtervarianttranches --- .../gatk4/filtervarianttranches/main.nf | 17 +++- .../filtervarianttranches/tests/main.nf.test | 78 +++++++++++++++++++ .../tests/main.nf.test.snap | 65 ++++++++++++++++ .../tests}/nextflow.config | 0 tests/config/pytest_modules.yml | 3 - .../gatk4/filtervarianttranches/main.nf | 26 ------- .../gatk4/filtervarianttranches/test.yml | 9 --- 7 files changed, 158 insertions(+), 40 deletions(-) create mode 100644 modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test.snap rename {tests/modules/nf-core/gatk4/filtervarianttranches => modules/nf-core/gatk4/filtervarianttranches/tests}/nextflow.config (100%) delete mode 100644 tests/modules/nf-core/gatk4/filtervarianttranches/main.nf delete mode 100644 tests/modules/nf-core/gatk4/filtervarianttranches/test.yml diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 2730938769e..837b6969287 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -27,7 +27,7 @@ process GATK4_FILTERVARIANTTRANCHES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def resources = resources.collect{"--resource $it"}.join(' ') + def resource_list = resources.collect{"--resource $it"}.join(' ') def avail_mem = 3072 if (!task.memory) { @@ -39,7 +39,7 @@ process GATK4_FILTERVARIANTTRANCHES { gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ FilterVariantTranches \\ --variant $vcf \\ - $resources \\ + $resource_list \\ --output ${prefix}.filtered.vcf.gz \\ --tmp-dir . \\ $args @@ -49,4 +49,17 @@ process GATK4_FILTERVARIANTTRANCHES { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo "" | gzip -c > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test new file mode 100644 index 00000000000..f1688c558e2 --- /dev/null +++ b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test @@ -0,0 +1,78 @@ +nextflow_process { + + name "Test Process GATK4_FILTERVARIANTTRANCHES" + script "../main.nf" + config "./nextflow.config" + process "GATK4_FILTERVARIANTTRANCHES" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/filtervarianttranches" + + test("homo sapiens - vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true), + [] + ] + input[1] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) + input[2] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[4] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[5] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + ).match() + } + ) + } + + } + + test("homo sapiens - vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true), + [] + ] + input[1] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) + input[2] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[4] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[5] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test.snap b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test.snap new file mode 100644 index 00000000000..8bc251b61cf --- /dev/null +++ b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test.snap @@ -0,0 +1,65 @@ +{ + "homo sapiens - vcf": { + "content": [ + [ + "versions.yml:md5,bad82b4b3eb370f70925cc069b16b63a" + ], + "test.filtered.vcf.gz", + "test.filtered.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T14:45:11.404254527" + }, + "homo sapiens - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,bad82b4b3eb370f70925cc069b16b63a" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,bad82b4b3eb370f70925cc069b16b63a" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T14:18:50.66032726" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/nextflow.config b/modules/nf-core/gatk4/filtervarianttranches/tests/nextflow.config similarity index 100% rename from tests/modules/nf-core/gatk4/filtervarianttranches/nextflow.config rename to modules/nf-core/gatk4/filtervarianttranches/tests/nextflow.config diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 0d111be9b62..bc58d6f400c 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -203,9 +203,6 @@ gatk4/cnnscorevariants: gatk4/determinegermlinecontigploidy: - modules/nf-core/gatk4/determinegermlinecontigploidy/** - tests/modules/nf-core/gatk4/determinegermlinecontigploidy/** -gatk4/filtervarianttranches: - - modules/nf-core/gatk4/filtervarianttranches/** - - tests/modules/nf-core/gatk4/filtervarianttranches/** gatk4/germlinecnvcaller: - modules/nf-core/gatk4/germlinecnvcaller/** - tests/modules/nf-core/gatk4/germlinecnvcaller/** diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf b/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf deleted file mode 100644 index 5b2b0d484b3..00000000000 --- a/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_FILTERVARIANTTRANCHES } from '../../../../../modules/nf-core/gatk4/filtervarianttranches/main.nf' -include { GATK4_CNNSCOREVARIANTS } from '../../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' -include { GATK4_HAPLOTYPECALLER } from '../../../../../modules/nf-core/gatk4/haplotypecaller/main.nf' -workflow test_gatk4_filtervarianttranches { - - resources = [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] - resources_index = [ - file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true), - ] - - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true), - [] - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - GATK4_FILTERVARIANTTRANCHES (input , resources, resources_index, fasta, fai, dict) -} diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/test.yml b/tests/modules/nf-core/gatk4/filtervarianttranches/test.yml deleted file mode 100644 index 23a782d05ef..00000000000 --- a/tests/modules/nf-core/gatk4/filtervarianttranches/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: gatk4 filtervarianttranches test_gatk4_filtervarianttranches - command: nextflow run ./tests/modules/nf-core/gatk4/filtervarianttranches -entry test_gatk4_filtervarianttranches -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filtervarianttranches/nextflow.config - tags: - - gatk4/filtervarianttranches - - gatk4 - files: - - path: output/gatk4/test.filtered.vcf.gz - - path: output/gatk4/test.filtered.vcf.gz.tbi - - path: output/gatk4/versions.yml From 80bca43321fb0f79fb9794472aab72e0f5aebabe Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Tue, 5 Nov 2024 09:10:30 +0000 Subject: [PATCH 11/59] migrate sitedepthtobaf --- modules/nf-core/gatk4/sitedepthtobaf/main.nf | 14 +++ .../gatk4/sitedepthtobaf/tests/main.nf.test | 107 ++++++++++++++++++ .../sitedepthtobaf/tests/main.nf.test.snap | 100 ++++++++++++++++ .../sitedepthtobaf/tests/nextflow.config | 5 + tests/config/pytest_modules.yml | 3 - .../nf-core/gatk4/sitedepthtobaf/main.nf | 41 ------- .../gatk4/sitedepthtobaf/nextflow.config | 9 -- .../nf-core/gatk4/sitedepthtobaf/test.yml | 35 ------ 8 files changed, 226 insertions(+), 88 deletions(-) create mode 100644 modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/sitedepthtobaf/tests/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/sitedepthtobaf/main.nf delete mode 100644 tests/modules/nf-core/gatk4/sitedepthtobaf/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/sitedepthtobaf/test.yml diff --git a/modules/nf-core/gatk4/sitedepthtobaf/main.nf b/modules/nf-core/gatk4/sitedepthtobaf/main.nf index b7d7c9eac61..185f56f9450 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/main.nf +++ b/modules/nf-core/gatk4/sitedepthtobaf/main.nf @@ -51,4 +51,18 @@ process GATK4_SITEDEPTHTOBAF { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo "" | gzip -c > ${prefix}.baf.txt.gz + touch ${prefix}.baf.txt.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + } diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test new file mode 100644 index 00000000000..ce0c13a1bf7 --- /dev/null +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test @@ -0,0 +1,107 @@ +nextflow_process { + + name "Test Process GATK4_SITEDEPTHTOBAF" + script "../main.nf" + config "./nextflow.config" + process "GATK4_SITEDEPTHTOBAF" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/sitedepthtobaf" + + setup { + run("GATK4_COLLECTSVEVIDENCE") { + script "../../collectsvevidence/main.nf" + process { + """ + vcf = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true) + tbi = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + + input[0] = Channel.of( + [ + [ id:'tumor', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + vcf, + tbi + ], + [ + [ id:'normal', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + vcf, + tbi + ] + ) + input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + } + + test("homo sapiens - bam - vcf") { + + when { + process { + """ + sitedepthtobaf_input = GATK4_COLLECTSVEVIDENCE.out.site_depths + .combine(GATK4_COLLECTSVEVIDENCE.out.site_depths_index, by:0) + .map({ meta, file, index -> [ [id:'test'], file, index ]}).groupTuple() + + input[0] = sitedepthtobaf_input + input[1] = [ + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + ] + input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[4] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - bam - vcf - stub") { + + options "-stub" + + when { + process { + """ + sitedepthtobaf_input = GATK4_COLLECTSVEVIDENCE.out.site_depths + .combine(GATK4_COLLECTSVEVIDENCE.out.site_depths_index, by:0) + .map({ meta, file, index -> [ [id:'test'], file, index ]}).groupTuple() + + input[0] = sitedepthtobaf_input + input[1] = [ + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + ] + input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[4] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap new file mode 100644 index 00000000000..22fe5bcb99d --- /dev/null +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap @@ -0,0 +1,100 @@ +{ + "homo sapiens - bam - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.baf.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.baf.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" + ], + "baf": [ + [ + { + "id": "test" + }, + "test.baf.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "baf_tbi": [ + [ + { + "id": "test" + }, + "test.baf.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-05T09:08:59.446700288" + }, + "homo sapiens - bam - vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.baf.txt.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.baf.txt.gz.tbi:md5,2f146ddadfd39ca5f1f2fd79f727d427" + ] + ], + "2": [ + "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" + ], + "baf": [ + [ + { + "id": "test" + }, + "test.baf.txt.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "baf_tbi": [ + [ + { + "id": "test" + }, + "test.baf.txt.gz.tbi:md5,2f146ddadfd39ca5f1f2fd79f727d427" + ] + ], + "versions": [ + "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-05T08:48:36.38848192" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/nextflow.config b/modules/nf-core/gatk4/sitedepthtobaf/tests/nextflow.config new file mode 100644 index 00000000000..1d90e59c76e --- /dev/null +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GATK4_COLLECTSVEVIDENCE { + ext.args = {"--sample-name ${meta.id}"} + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index bc58d6f400c..7505a9bb424 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -212,9 +212,6 @@ gatk4/postprocessgermlinecnvcalls: gatk4/selectsamples: - modules/nf-core/gatk4/selectsamples/** - tests/modules/nf-core/gatk4/selectsamples/** -gatk4/sitedepthtobaf: - - modules/nf-core/gatk4/sitedepthtobaf/** - - tests/modules/nf-core/gatk4/sitedepthtobaf/** gatk4/variantrecalibrator: - modules/nf-core/gatk4/variantrecalibrator/** - tests/modules/nf-core/gatk4/variantrecalibrator/** diff --git a/tests/modules/nf-core/gatk4/sitedepthtobaf/main.nf b/tests/modules/nf-core/gatk4/sitedepthtobaf/main.nf deleted file mode 100644 index 734e2ccde01..00000000000 --- a/tests/modules/nf-core/gatk4/sitedepthtobaf/main.nf +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_SITEDEPTHTOBAF } from '../../../../../modules/nf-core/gatk4/sitedepthtobaf/main.nf' -include { GATK4_COLLECTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' - -workflow test_gatk4_sitedepthtobaf { - - vcf = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true) - tbi = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) - - input = Channel.of([ - [ id:'tumor', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - vcf, - tbi - ], - [ - [ id:'normal', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - vcf, - tbi - ] - ) - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - - GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict ) - - sitedepthtobaf_input = GATK4_COLLECTSVEVIDENCE.out.site_depths - .combine(GATK4_COLLECTSVEVIDENCE.out.site_depths_index, by:0) - .map({ meta, file, index -> [ [id:'test'], file, index ]}).groupTuple() - - GATK4_SITEDEPTHTOBAF ( sitedepthtobaf_input, [ vcf, tbi ], fasta, fasta_fai, dict ) -} diff --git a/tests/modules/nf-core/gatk4/sitedepthtobaf/nextflow.config b/tests/modules/nf-core/gatk4/sitedepthtobaf/nextflow.config deleted file mode 100644 index 54136c7018b..00000000000 --- a/tests/modules/nf-core/gatk4/sitedepthtobaf/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GATK4_COLLECTSVEVIDENCE { - ext.args = {"--sample-name ${meta.id}"} - } - -} diff --git a/tests/modules/nf-core/gatk4/sitedepthtobaf/test.yml b/tests/modules/nf-core/gatk4/sitedepthtobaf/test.yml deleted file mode 100644 index 16ce5b445fc..00000000000 --- a/tests/modules/nf-core/gatk4/sitedepthtobaf/test.yml +++ /dev/null @@ -1,35 +0,0 @@ -- name: gatk4 sitedepthtobaf test_gatk4_sitedepthtobaf - command: nextflow run ./tests/modules/nf-core/gatk4/sitedepthtobaf -entry test_gatk4_sitedepthtobaf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/sitedepthtobaf/nextflow.config - tags: - - gatk4/sitedepthtobaf - - gatk4 - files: - - path: output/gatk4/normal.pe.txt.gz - md5sum: aa7489b9024c8ac39c39a5f020b98d1c - - path: output/gatk4/normal.pe.txt.gz.tbi - md5sum: 99324af842f3236a1e78703d06992648 - - path: output/gatk4/normal.sd.txt.gz - md5sum: b83b89a84e35a0b071ce2bbba84c7ca7 - - path: output/gatk4/normal.sd.txt.gz.tbi - md5sum: bff6f3811b84019316ee8e5b6c9ab9bb - - path: output/gatk4/normal.sr.txt.gz - md5sum: 2881e2e9fa1b9b6c02f0a756e25ff96a - - path: output/gatk4/normal.sr.txt.gz.tbi - md5sum: 8207e46090fdbe125ce6936ac383da40 - - path: output/gatk4/test.baf.txt.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: output/gatk4/test.baf.txt.gz.tbi - md5sum: 2f146ddadfd39ca5f1f2fd79f727d427 - - path: output/gatk4/tumor.pe.txt.gz - md5sum: 566a9621ff7ee1d12e7593d953db5344 - - path: output/gatk4/tumor.pe.txt.gz.tbi - md5sum: 513329f5ba4b6c982f03beea47a8ba53 - - path: output/gatk4/tumor.sd.txt.gz - md5sum: bd90f752f403f054abf64bddf4433f6c - - path: output/gatk4/tumor.sd.txt.gz.tbi - md5sum: 4a4dba7c9060ac0206f123d0ab2cb733 - - path: output/gatk4/tumor.sr.txt.gz - md5sum: b95035ddc709ed6602624459600c4d47 - - path: output/gatk4/tumor.sr.txt.gz.tbi - md5sum: 33b3a9ff444eb0e0fc3016239651f05f - - path: output/gatk4/versions.yml From 68c8cdb37921ec5364ad8001466ff21fc6b20b1b Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Tue, 5 Nov 2024 09:45:35 +0000 Subject: [PATCH 12/59] migrate germlinecnvcaller - intermediate commit --- .../nf-core/gatk4/germlinecnvcaller/README.md | 9 -- .../nf-core/gatk4/germlinecnvcaller/main.nf | 8 -- .../germlinecnvcaller/tests/main.nf.test | 116 ++++++++++++++++++ .../germlinecnvcaller/tests/nextflow.config | 11 ++ tests/config/pytest_modules.yml | 3 - .../nf-core/gatk4/germlinecnvcaller/main.nf | 65 ---------- .../gatk4/germlinecnvcaller/nextflow.config | 21 ---- .../nf-core/gatk4/germlinecnvcaller/test.yml | 21 ---- 8 files changed, 127 insertions(+), 127 deletions(-) delete mode 100644 modules/nf-core/gatk4/germlinecnvcaller/README.md create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/germlinecnvcaller/main.nf delete mode 100644 tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/germlinecnvcaller/test.yml diff --git a/modules/nf-core/gatk4/germlinecnvcaller/README.md b/modules/nf-core/gatk4/germlinecnvcaller/README.md deleted file mode 100644 index c6a4545655a..00000000000 --- a/modules/nf-core/gatk4/germlinecnvcaller/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index 5a184ca2c71..36749493b7f 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -20,10 +20,6 @@ process GATK4_GERMLINECNVCALLER { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def intervals_command = intervals ? "--intervals ${intervals}" : "" @@ -60,10 +56,6 @@ process GATK4_GERMLINECNVCALLER { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." - } def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir -p ${prefix}-cnv-calls/${prefix}-calls diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test new file mode 100644 index 00000000000..c8a713214ed --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -0,0 +1,116 @@ +nextflow_process { + + name "Test Process GATK4_GERMLINECNVCALLER" + script "../main.nf" + config "./nextflow.config" + process "GATK4_GERMLINECNVCALLER" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectreadcounts" + tag "gatk4/germlinecnvcaller" + + setup { + run("GATK4_COLLECTREADCOUNTS") { + script "../../collectreadcounts/main.nf" + process { + """ + input[0] = Channel.of( + [ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + ]) + input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists:true)]) + input[3] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]) + + """ + } + } + run("GATK4_DETERMINEGERMLINECONTIGPLOIDY") { + script "../../determinegermlinecontigploidy/main.nf" + process { + """ + bed = file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists:true) + + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[:], tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) + input[1] = [[],[]] + input[2] = contig_ploidy_table + """ + } + } + run("GATK4_BEDTOINTERVALLIST") { + script "../../bedtointervallist/main.nf" + process { + """ + input[0] = Channel.of([ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) + input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]) + """ + } + } + } + + test("homo sapiens - bam") { + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[:] , tsv ]}) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map{ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [ , tsv ]}) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map{ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config b/modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config new file mode 100644 index 00000000000..d1b64bf4f03 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: 'GATK4_COLLECTREADCOUNTS*' { + ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" + } + withName: 'GATK4_DETERMINEGERMLINECONTIGPLOIDY' { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY" + } + withName: 'GATK4_GERMLINECNVCALLER' { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY --run-mode COHORT" + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 7505a9bb424..74cc3b2f838 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -203,9 +203,6 @@ gatk4/cnnscorevariants: gatk4/determinegermlinecontigploidy: - modules/nf-core/gatk4/determinegermlinecontigploidy/** - tests/modules/nf-core/gatk4/determinegermlinecontigploidy/** -gatk4/germlinecnvcaller: - - modules/nf-core/gatk4/germlinecnvcaller/** - - tests/modules/nf-core/gatk4/germlinecnvcaller/** gatk4/postprocessgermlinecnvcalls: - modules/nf-core/gatk4/postprocessgermlinecnvcalls/** - tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/** diff --git a/tests/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/tests/modules/nf-core/gatk4/germlinecnvcaller/main.nf deleted file mode 100644 index 1908a1cb32d..00000000000 --- a/tests/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/gatk4/bedtointervallist/main.nf' -include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' -include { GATK4_DETERMINEGERMLINECONTIGPLOIDY as GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT } from '../../../../../modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf' -include { GATK4_GERMLINECNVCALLER as GATK4_GERMLINECNVCALLER_COHORT } from '../../../../../modules/nf-core/gatk4/germlinecnvcaller/main.nf' -include { GATK4_GERMLINECNVCALLER as GATK4_GERMLINECNVCALLER_CASE } from '../../../../../modules/nf-core/gatk4/germlinecnvcaller/main.nf' - -workflow test_gatk4_germlinecnvcaller { - input = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true), - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) - ]) - - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) - - bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) - - GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT ( - GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ] }) - .groupTuple() - .combine(bed) - .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), - [[],[]], - contig_ploidy_table - ) - - intervals = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) - ] - GATK4_BEDTOINTERVALLIST ( intervals, dict ) - - gcnvc_cohort_input = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ]}) - .groupTuple() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) - .map{ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]} - - GATK4_GERMLINECNVCALLER_COHORT ( gcnvc_cohort_input ) - - gcnvc_case_input = GATK4_COLLECTREADCOUNTS.out.tsv.first() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .map{ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]} - GATK4_GERMLINECNVCALLER_CASE ( gcnvc_case_input ) - -} diff --git a/tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config b/tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config deleted file mode 100644 index 88f61a49e11..00000000000 --- a/tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config +++ /dev/null @@ -1,21 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: 'GATK4_COLLECTREADCOUNTS*' { - ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" - } - - withName: 'GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT' { - ext.args = "--interval-merging-rule OVERLAPPING_ONLY" - } - - withName: 'GATK4_GERMLINECNVCALLER_COHORT' { - ext.args = "--interval-merging-rule OVERLAPPING_ONLY --run-mode COHORT" - } - - withName: 'GATK4_GERMLINECNVCALLER_CASE' { - ext.args = "--run-mode CASE" - } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/germlinecnvcaller/test.yml b/tests/modules/nf-core/gatk4/germlinecnvcaller/test.yml deleted file mode 100644 index f78fbfafb86..00000000000 --- a/tests/modules/nf-core/gatk4/germlinecnvcaller/test.yml +++ /dev/null @@ -1,21 +0,0 @@ -- name: gatk4 germlinecnvcaller test_gatk4_germlinecnvcaller - command: nextflow run ./tests/modules/nf-core/gatk4/germlinecnvcaller -entry test_gatk4_germlinecnvcaller -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config - tags: - - gatk4/germlinecnvcaller - - gatk4 - files: - - path: output/gatk4/test-cnv-model/test-model - - path: output/gatk4/test-cnv-model/test-calls - - path: output/gatk4/test-cnv-calls/test-calls - - path: output/gatk4/versions.yml - -- name: gatk4 germlinecnvcaller test_gatk4_germlinecnvcaller_stub - command: nextflow run ./tests/modules/nf-core/gatk4/germlinecnvcaller -entry test_gatk4_germlinecnvcaller -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config -stub - tags: - - gatk4/germlinecnvcaller - - gatk4 - files: - - path: output/gatk4/test-cnv-model/test-model - - path: output/gatk4/test-cnv-model/test-calls - - path: output/gatk4/test-cnv-calls/test-calls - - path: output/gatk4/versions.yml From 0d98cacca1347f7b2f834e35adb7945ae014e40e Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Wed, 6 Nov 2024 09:09:43 +0000 Subject: [PATCH 13/59] ben made me do it --- .../nf-core/gatk4/cnnscorevariants/main.nf | 20 +++++++++++++------ .../nf-core/gatk4/mergemutectstats/main.nf | 2 +- .../gatk4/svannotate/tests/nextflow.config | 6 ------ .../gatk4/svcluster/tests/nextflow.config | 6 ------ 4 files changed, 15 insertions(+), 19 deletions(-) delete mode 100644 modules/nf-core/gatk4/svannotate/tests/nextflow.config delete mode 100644 modules/nf-core/gatk4/svcluster/tests/nextflow.config diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf index 92de2267e06..6f1a0466f96 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -28,10 +28,10 @@ process GATK4_CNNSCOREVARIANTS { } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def aligned_input = aligned_input ? "--input $aligned_input" : "" + def aligned_input_cmd = aligned_input ? "--input $aligned_input" : "" def interval_command = intervals ? "--intervals $intervals" : "" - def architecture = architecture ? "--architecture $architecture" : "" - def weights = weights ? "--weights $weights" : "" + def architecture_cmd = architecture ? "--architecture $architecture" : "" + def weights_cmd = weights ? "--weights $weights" : "" def avail_mem = 3072 if (!task.memory) { @@ -48,9 +48,9 @@ process GATK4_CNNSCOREVARIANTS { --output ${prefix}.cnn.vcf.gz \\ --reference $fasta \\ $interval_command \\ - $aligned_input \\ - $architecture \\ - $weights \\ + $aligned_input_cmd \\ + $architecture_cmd \\ + $weights_cmd \\ --tmp-dir . \\ $args @@ -59,4 +59,12 @@ process GATK4_CNNSCOREVARIANTS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo "" | gzip -c > ${prefix}.cnn.vcf.gz + touch ${prefix}.cnn.vcf.gz.tbi + """ } diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 1a500fc1f88..aa74d551fac 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -19,7 +19,7 @@ process GATK4_MERGEMUTECTSTATS { script: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def input_list = stats.collect{ "--stats ${it}"}.join(' ') def avail_mem = 3072 diff --git a/modules/nf-core/gatk4/svannotate/tests/nextflow.config b/modules/nf-core/gatk4/svannotate/tests/nextflow.config deleted file mode 100644 index 11ec85a5fc3..00000000000 --- a/modules/nf-core/gatk4/svannotate/tests/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - withName: MANTA_GERMLINE { - enabled: false - ] - } -} diff --git a/modules/nf-core/gatk4/svcluster/tests/nextflow.config b/modules/nf-core/gatk4/svcluster/tests/nextflow.config deleted file mode 100644 index 11ec85a5fc3..00000000000 --- a/modules/nf-core/gatk4/svcluster/tests/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - withName: MANTA_GERMLINE { - enabled: false - ] - } -} From e37803b2a9da7f13f63493d8d0d6ec9fd4f56e7a Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Wed, 6 Nov 2024 09:49:52 +0000 Subject: [PATCH 14/59] migrate createreadcountpanelofnormals --- .../createreadcountpanelofnormals/main.nf | 1 - .../tests/main.nf.test | 102 ++++++++++++++++++ .../tests/main.nf.test.snap | 48 +++++++++ .../tests}/nextflow.config | 1 + .../createreadcountpanelofnormals/main.nf | 37 ------- .../createreadcountpanelofnormals/test.yml | 17 --- 6 files changed, 151 insertions(+), 55 deletions(-) create mode 100644 modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap rename {tests/modules/nf-core/gatk4/createreadcountpanelofnormals => modules/nf-core/gatk4/createreadcountpanelofnormals/tests}/nextflow.config (67%) delete mode 100644 tests/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf delete mode 100644 tests/modules/nf-core/gatk4/createreadcountpanelofnormals/test.yml diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf index a31a20d0b44..ab22a949721 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf @@ -42,7 +42,6 @@ process GATK4_CREATEREADCOUNTPANELOFNORMALS { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.hdf5 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test new file mode 100644 index 00000000000..55b725861eb --- /dev/null +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test @@ -0,0 +1,102 @@ +nextflow_process { + + name "Test Process GATK4_CREATEREADCOUNTPANELOFNORMALS" + script "../main.nf" + config "./nextflow.config" + process "GATK4_CREATEREADCOUNTPANELOFNORMALS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/preprocessintervals" + tag "gatk4/collectreadcounts" + tag "gatk4/createreadcountpanelofnormals" + + setup { + run("GATK4_PREPROCESSINTERVALS") { + script "../../preprocessintervals/main.nf" + process { + """ + fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'],checkIfExists: true)]).collect() + fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'],checkIfExists: true)]).collect() + dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'],checkIfExists: true)]).collect() + + input[0] = fasta + input[1] = fai + input[2] = dict + input[3] = [[],[]] + input[4] = [[],[]] + """ + } + } + run("GATK4_COLLECTREADCOUNTS") { + script "../../collectreadcounts/main.nf" + process { + """ + intervals = GATK4_PREPROCESSINTERVALS.out.interval_list.map{ meta, list -> list} + input[0] = Channel.of([ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + ], + [ + [ id:'test2', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + ]) + .combine(intervals) + input[1] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'],checkIfExists: true)]).collect() + input[2] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'],checkIfExists: true)]).collect() + input[3] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'],checkIfExists: true)]).collect() + """ + } + } + } + + test("homo sapiens - bam") { + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.pon[0][1]).name + ).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[:], tsv ] }) + .groupTuple() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap new file mode 100644 index 00000000000..dd30f8981af --- /dev/null +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "homo sapiens - bam": { + "content": [ + [ + "versions.yml:md5,3b00a427858f3b991cc03fe6b467fe9d" + ], + "test.hdf5" + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T09:28:03.932486659" + }, + "homo sapiens - bam - stub": { + "content": [ + { + "0": [ + [ + { + + }, + "null.hdf5:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3b00a427858f3b991cc03fe6b467fe9d" + ], + "pon": [ + [ + { + + }, + "null.hdf5:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3b00a427858f3b991cc03fe6b467fe9d" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T09:11:09.743925974" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/nextflow.config similarity index 67% rename from tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config rename to modules/nf-core/gatk4/createreadcountpanelofnormals/tests/nextflow.config index a8c5250b024..90cfd3c7dc7 100644 --- a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/nextflow.config @@ -1,3 +1,4 @@ +docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } diff --git a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf b/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf deleted file mode 100644 index f45144db259..00000000000 --- a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf +++ /dev/null @@ -1,37 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_CREATEREADCOUNTPANELOFNORMALS } from '../../../../../modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf' -include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' -include { GATK4_PREPROCESSINTERVALS } from '../../../../../modules/nf-core/gatk4/preprocessintervals/main.nf' - -workflow test_gatk4_createreadcountpanelofnormals { - - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() - - GATK4_PREPROCESSINTERVALS ( fasta, fai, dict, [[],[]], [[],[]]).interval_list - .map {meta,list -> list} - .set {ch_intervals} - - input = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - ]).combine(ch_intervals) - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) - - GATK4_CREATEREADCOUNTPANELOFNORMALS ( - GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ] }) - .groupTuple() - ) -} diff --git a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/test.yml b/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/test.yml deleted file mode 100644 index 829079feaa5..00000000000 --- a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: "gatk4 createreadcountpanelofnormals" - command: nextflow run ./tests/modules/nf-core/gatk4/createreadcountpanelofnormals -entry test_gatk4_createreadcountpanelofnormals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config - tags: - - "gatk4" - - "gatk4/createreadcountpanelofnormals" - files: - - path: "output/gatk4/test.hdf5" - - path: "output/gatk4/versions.yml" - -- name: "gatk4 createreadcountpanelofnormals stub" - command: nextflow run ./tests/modules/nf-core/gatk4/createreadcountpanelofnormals -entry test_gatk4_createreadcountpanelofnormals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config -stub - tags: - - "gatk4" - - "gatk4/createreadcountpanelofnormals" - files: - - path: "output/gatk4/test.hdf5" - - path: "output/gatk4/versions.yml" From f851bab7ebf5310475c7a262ff7644f2cd3b3d39 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Wed, 6 Nov 2024 10:32:45 +0000 Subject: [PATCH 15/59] more nf-test --- .../determinegermlinecontigploidy/README.md | 9 - .../determinegermlinecontigploidy/main.nf | 8 - .../tests/main.nf.test | 104 +++++++++++ .../tests/main.nf.test.snap | 80 +++++++++ .../tests}/nextflow.config | 5 - .../gatk4/variantrecalibrator/tests/AS.config | 7 + .../variantrecalibrator/tests/main.nf.test | 167 ++++++++++++++++++ .../tests/main.nf.test.snap | 133 ++++++++++++++ .../variantrecalibrator/tests/noAS.config | 4 - tests/config/pytest_modules.yml | 6 - .../determinegermlinecontigploidy/main.nf | 89 ---------- .../determinegermlinecontigploidy/test.yml | 31 ---- .../gatk4/postprocessgermlinecnvcalls/main.nf | 2 +- .../nf-core/gatk4/variantrecalibrator/main.nf | 72 -------- .../gatk4/variantrecalibrator/test.yml | 27 --- 15 files changed, 492 insertions(+), 252 deletions(-) delete mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/README.md create mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap rename {tests/modules/nf-core/gatk4/determinegermlinecontigploidy => modules/nf-core/gatk4/determinegermlinecontigploidy/tests}/nextflow.config (70%) create mode 100644 modules/nf-core/gatk4/variantrecalibrator/tests/AS.config create mode 100644 modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test.snap rename tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config => modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config (64%) delete mode 100644 tests/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf delete mode 100644 tests/modules/nf-core/gatk4/determinegermlinecontigploidy/test.yml delete mode 100644 tests/modules/nf-core/gatk4/variantrecalibrator/main.nf delete mode 100644 tests/modules/nf-core/gatk4/variantrecalibrator/test.yml diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md b/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md deleted file mode 100644 index c6a4545655a..00000000000 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index 6e5c9b211a1..c4183bdd5bd 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -22,10 +22,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def intervals = bed ? "--intervals ${bed}" : "" @@ -64,10 +60,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." - } prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}-calls diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test new file mode 100644 index 00000000000..aa4583c3bc9 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -0,0 +1,104 @@ +nextflow_process { + + name "Test Process GATK4_DETERMINEGERMLINECONTIGPLOIDY" + script "../main.nf" + config "./nextflow.config" + process "GATK4_DETERMINEGERMLINECONTIGPLOIDY" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + + setup { + run("GATK4_COLLECTREADCOUNTS") { + script "../../collectreadcounts/main.nf" + process { + """ + bed = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) + + ch_input = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true) + ]).combine(bed) + + ch_fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() + ch_fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() + ch_dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() + + input = [ch_input, ch_fasta, ch_fai, ch_dict] + """ + } + } + } + + test("homo sapiens - bam") { + + when { + process { + """ + contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) + bed = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) + .map({bed -> return bed.text.replaceFirst("0","10001") }) + .collectFile( name: "genome_exclude.bed" ) + + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'] , tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, [], bed ]}) + input[1] = [[],[]] + input[2] = contig_ploidy_table + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) + bed = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) + .map({bed -> return bed.text.replaceFirst("0","10001") }) + .collectFile( name: "genome_exclude.bed" ) + + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'] , tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, [], bed ]}) + input[1] = [[],[]] + input[2] = contig_ploidy_table + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap new file mode 100644 index 00000000000..3f480c2bf99 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap @@ -0,0 +1,80 @@ +{ + "homo sapiens - bam": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + + ], + "calls": [ + + ], + "model": [ + + ], + "versions": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:22:21.007041155" + }, + "homo sapiens - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test-calls:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test-model:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" + ], + "calls": [ + [ + { + "id": "test" + }, + "test-calls:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "model": [ + [ + { + "id": "test" + }, + "test-model:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:23:35.989186048" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config similarity index 70% rename from tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config rename to modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config index a764fa9cc73..c2455205820 100644 --- a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config @@ -1,13 +1,8 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: GATK4_COLLECTREADCOUNTS { ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" } - withName: GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT { ext.args = "--interval-merging-rule OVERLAPPING_ONLY" } - } diff --git a/modules/nf-core/gatk4/variantrecalibrator/tests/AS.config b/modules/nf-core/gatk4/variantrecalibrator/tests/AS.config new file mode 100644 index 00000000000..eadb336e9db --- /dev/null +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/AS.config @@ -0,0 +1,7 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + withName: GATK4_VARIANTRECALIBRATOR { + ext.args = '-mode SNP -an QD -an MQ -an FS -AS' + } +} diff --git a/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test new file mode 100644 index 00000000000..d0878ab7fec --- /dev/null +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test @@ -0,0 +1,167 @@ +nextflow_process { + + name "Test Process GATK4_VARIANTRECALIBRATOR" + script "../main.nf" + process "GATK4_VARIANTRECALIBRATOR" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/variantrecalibrator" + + test("homo sapiens - vcf - allele specificity") { + config "./AS.config" + when { + process { + """ + input_vcf = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) + ] + + resources_vcf = [ + file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) + ] + resources_tbi = [ + file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) + ] + labels = [ + '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', + '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', + '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', + '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + + input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.recal[0][1]).name, + file(process.out.idx[0][1]).name, + process.out.tranches, + process.out.plots, + ).match() } + ) + } + + } + + test("homo sapiens - vcf - no allele specificity") { + config "./noAS.config" + when { + process { + """ + input_vcf = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) + ] + + resources_vcf = [ + file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) + ] + resources_tbi = [ + file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) + ] + labels = [ + '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', + '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', + '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', + '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + + input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.recal[0][1]).name, + file(process.out.idx[0][1]).name, + process.out.tranches, + process.out.plots, + ).match() } + ) + } + + } + + test("homo sapiens - vcf - stub") { + + options "-stub" + + when { + process { + """ + input_vcf = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) + ] + + resources_vcf = [ + file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) + ] + resources_tbi = [ + file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) + ] + labels = [ + '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', + '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', + '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', + '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + + input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test.snap new file mode 100644 index 00000000000..62882f25faa --- /dev/null +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test.snap @@ -0,0 +1,133 @@ +{ + "homo sapiens - vcf - allele specificity": { + "content": [ + [ + "versions.yml:md5,fb9c98d8bd2f8335179f7c037c63bb0d" + ], + "test.recal", + "test.recal.idx", + [ + [ + { + "id": "test" + }, + "test.tranches:md5,ad52fa69325c758f458a30ee5b43d6b5" + ] + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:19:03.416258473" + }, + "homo sapiens - vcf - no allele specificity": { + "content": [ + [ + "versions.yml:md5,fb9c98d8bd2f8335179f7c037c63bb0d" + ], + "test.recal", + "test.recal.idx", + [ + [ + { + "id": "test" + }, + "test.tranches:md5,c029e52fd63a893e1154cc9144a19eeb" + ] + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:26:53.032044124" + }, + "homo sapiens - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.recal:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.idx:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.tranches:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "testplots.R:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,fb9c98d8bd2f8335179f7c037c63bb0d" + ], + "idx": [ + [ + { + "id": "test" + }, + "test.idx:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "plots": [ + [ + { + "id": "test" + }, + "testplots.R:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "recal": [ + [ + { + "id": "test" + }, + "test.recal:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tranches": [ + [ + { + "id": "test" + }, + "test.tranches:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,fb9c98d8bd2f8335179f7c037c63bb0d" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:14:43.858797367" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config b/modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config similarity index 64% rename from tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config rename to modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config index e51b90449a5..69efa09ea86 100644 --- a/tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config @@ -5,8 +5,4 @@ process { withName: GATK4_VARIANTRECALIBRATOR { ext.args = '-mode SNP -an QD -an MQ -an FS -an SOR' } - - withName: GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY { - ext.args = '-mode SNP -an QD -an MQ -an FS -AS' - } } diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 74cc3b2f838..baf287515d1 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -200,18 +200,12 @@ gatk/indelrealigner: gatk4/cnnscorevariants: - modules/nf-core/gatk4/cnnscorevariants/** - tests/modules/nf-core/gatk4/cnnscorevariants/** -gatk4/determinegermlinecontigploidy: - - modules/nf-core/gatk4/determinegermlinecontigploidy/** - - tests/modules/nf-core/gatk4/determinegermlinecontigploidy/** gatk4/postprocessgermlinecnvcalls: - modules/nf-core/gatk4/postprocessgermlinecnvcalls/** - tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/** gatk4/selectsamples: - modules/nf-core/gatk4/selectsamples/** - tests/modules/nf-core/gatk4/selectsamples/** -gatk4/variantrecalibrator: - - modules/nf-core/gatk4/variantrecalibrator/** - - tests/modules/nf-core/gatk4/variantrecalibrator/** gatk4spark/baserecalibrator: - modules/nf-core/gatk4spark/baserecalibrator/** - tests/modules/nf-core/gatk4spark/baserecalibrator/** diff --git a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf deleted file mode 100644 index 508a4d3caf0..00000000000 --- a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_DETERMINEGERMLINECONTIGPLOIDY as GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT } from '../../../../../modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf' -include { GATK4_DETERMINEGERMLINECONTIGPLOIDY as GATK4_DETERMINEGERMLINECONTIGPLOIDY_CASE } from '../../../../../modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf' -include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' - -workflow test_gatk4_determinegermlinecontigploidy { - - input = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true), - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) - ]) - - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) - - bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) - - GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT ( - GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ] }) - .groupTuple() - .combine(bed) - .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), - [[],[]], - contig_ploidy_table - ) - - GATK4_DETERMINEGERMLINECONTIGPLOIDY_CASE ( - GATK4_COLLECTREADCOUNTS.out.tsv - .first() - .map({ meta, tsv -> [ [id:'test_case'], tsv, [], [] ] }), - GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.model, - [] - ) -} - -workflow test_gatk4_determinegermlinecontigploidy_cohort_exclude_intervals { - - bed_1 = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) - .map({bed -> return bed.text.replace("40001","10001") + "chr22\t10001\t40001\n" }) - .collectFile( name: "genome.bed" ) - - input = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true) - ]).combine(bed_1) - - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) - - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) - bed_2 = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) - .map({bed -> return bed.text.replaceFirst("0","10001") }) - .collectFile( name: "genome_exclude.bed" ) - - GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT ( - GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ] }) - .groupTuple() - .combine(bed_2) - .map({ meta, counts, bed -> [ meta, counts, [], bed ]}), - [[],[]], - contig_ploidy_table - ) -} diff --git a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/test.yml b/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/test.yml deleted file mode 100644 index 5f42e6e43cf..00000000000 --- a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/test.yml +++ /dev/null @@ -1,31 +0,0 @@ -- name: gatk4 determinegermlinecontigploidy test_gatk4_determinegermlinecontigploidy - command: nextflow run ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy -entry test_gatk4_determinegermlinecontigploidy -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config - tags: - - gatk4/determinegermlinecontigploidy - - gatk4 - files: - - path: output/gatk4/test-calls - - path: output/gatk4/test-model - - path: output/gatk4/test_case-calls - - path: output/gatk4/versions.yml - -- name: gatk4 determinegermlinecontigploidy test_gatk4_determinegermlinecontigploidy_cohort_exclude_intervals - command: nextflow run ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy -entry test_gatk4_determinegermlinecontigploidy_cohort_exclude_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config - tags: - - gatk4/determinegermlinecontigploidy - - gatk4 - files: - - path: output/gatk4/test-calls - - path: output/gatk4/test-model - - path: output/gatk4/versions.yml - -- name: gatk4 determinegermlinecontigploidy test_gatk4_determinegermlinecontigploidy_stub - command: nextflow run ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy -entry test_gatk4_determinegermlinecontigploidy -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config -stub - tags: - - gatk4/determinegermlinecontigploidy - - gatk4 - files: - - path: output/gatk4/test-calls - - path: output/gatk4/test-model - - path: output/gatk4/test_case-calls - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index e6314d6c045..de83628743d 100644 --- a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -11,7 +11,7 @@ include { GATK4_POSTPROCESSGERMLINECNVCALLS as GATK4_POSTPROCESSGERMLINECNVCALLS include { GATK4_POSTPROCESSGERMLINECNVCALLS as GATK4_POSTPROCESSGERMLINECNVCALLS_CASE } from '../../../../../modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf' workflow test_gatk4_postprocessgermlinecnvcalls { - input = Channel.of([ + input = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf b/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf deleted file mode 100644 index f8680f9dec1..00000000000 --- a/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ /dev/null @@ -1,72 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY } from '../../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' -include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' - -workflow test_gatk4_variantrecalibrator { - - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) - ] - - resources_vcf = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) - ] - resources_tbi = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) - ] - labels = [ - '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', - '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', - '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', - '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - - GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY(input, resources_vcf, resources_tbi, labels, fasta, fai, dict) -} - -workflow test_gatk4_variantrecalibrator_allele_specific { - - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) - ] - - resources_vcf = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) - ] - resources_tbi = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) - ] - labels = [ - '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', - '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', - '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', - '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - - GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY(input, resources_vcf, resources_tbi, labels, fasta, fai, dict) -} diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml b/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml deleted file mode 100644 index b24b45cbe13..00000000000 --- a/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml +++ /dev/null @@ -1,27 +0,0 @@ -- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator - command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config - tags: - - gatk4 - - gatk4/variantrecalibrator - files: - - path: output/gatk4/test.recal - contains: - - "#CHROM POS ID REF ALT QUAL FILTER INFO" - - path: output/gatk4/test.recal.idx - - path: output/gatk4/test.tranches - md5sum: c029e52fd63a893e1154cc9144a19eeb - - path: output/gatk4/versions.yml - -- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific - command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator_allele_specific -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config - tags: - - gatk4 - - gatk4/variantrecalibrator - files: - - path: output/gatk4/test.recal - contains: - - "#CHROM POS ID REF ALT QUAL FILTER INFO" - - path: output/gatk4/test.recal.idx - - path: output/gatk4/test.tranches - md5sum: ad52fa69325c758f458a30ee5b43d6b5 - - path: output/gatk4/versions.yml From 0aa1865bb8f6656d34b1e34e8bce32bc267f2cf8 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Wed, 6 Nov 2024 12:14:20 +0000 Subject: [PATCH 16/59] more nf-test --- .../nf-core/gatk4/cnnscorevariants/README.md | 9 - .../gatk4/cnnscorevariants/environment.yml | 5 + .../nf-core/gatk4/cnnscorevariants/main.nf | 5 + .../gatk4/cnnscorevariants/tests/main.nf.test | 77 ++++++++ .../cnnscorevariants/tests/main.nf.test.snap | 65 +++++++ .../postprocessgermlinecnvcalls/README.md | 9 - .../environment.yml | 5 + .../gatk4/postprocessgermlinecnvcalls/main.nf | 15 +- .../tests/main.nf.test | 140 +++++++++++++++ .../tests/main.nf.test.snap | 102 +++++++++++ .../tests}/nextflow.config | 7 - .../gatk4spark/applybqsr/environment.yml | 2 +- modules/nf-core/gatk4spark/applybqsr/main.nf | 4 +- .../applybqsr/tests/main.nf.test.snap | 40 ++--- .../baserecalibrator/environment.yml | 2 +- .../gatk4spark/baserecalibrator/main.nf | 16 +- .../baserecalibrator/tests/main.nf.test | 160 +++++++++++++++++ .../baserecalibrator/tests/main.nf.test.snap | 167 ++++++++++++++++++ .../baserecalibrator/tests/nextflow.config | 2 + .../gatk4spark/markduplicates/environment.yml | 2 +- .../nf-core/gatk4spark/markduplicates/main.nf | 4 +- .../markduplicates/tests/main.nf.test.snap | 48 ++--- tests/config/pytest_modules.yml | 9 - .../nf-core/gatk4/cnnscorevariants/main.nf | 19 -- .../gatk4/cnnscorevariants/nextflow.config | 5 - .../nf-core/gatk4/cnnscorevariants/test.yml | 10 -- .../gatk4/postprocessgermlinecnvcalls/main.nf | 85 --------- .../postprocessgermlinecnvcalls/test.yml | 21 --- .../gatk4spark/baserecalibrator/main.nf | 69 -------- .../baserecalibrator/nextflow.config | 5 - .../gatk4spark/baserecalibrator/test.yml | 39 ---- 31 files changed, 798 insertions(+), 350 deletions(-) delete mode 100644 modules/nf-core/gatk4/cnnscorevariants/README.md create mode 100644 modules/nf-core/gatk4/cnnscorevariants/environment.yml create mode 100644 modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap delete mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md create mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml create mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap rename {tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls => modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests}/nextflow.config (82%) create mode 100644 modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test create mode 100644 modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4spark/baserecalibrator/tests/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/cnnscorevariants/main.nf delete mode 100644 tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4/cnnscorevariants/test.yml delete mode 100644 tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf delete mode 100644 tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/test.yml delete mode 100644 tests/modules/nf-core/gatk4spark/baserecalibrator/main.nf delete mode 100644 tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config delete mode 100644 tests/modules/nf-core/gatk4spark/baserecalibrator/test.yml diff --git a/modules/nf-core/gatk4/cnnscorevariants/README.md b/modules/nf-core/gatk4/cnnscorevariants/README.md deleted file mode 100644 index c6a4545655a..00000000000 --- a/modules/nf-core/gatk4/cnnscorevariants/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/cnnscorevariants/environment.yml b/modules/nf-core/gatk4/cnnscorevariants/environment.yml new file mode 100644 index 00000000000..e93eac37506 --- /dev/null +++ b/modules/nf-core/gatk4/cnnscorevariants/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf index 6f1a0466f96..5ff13b41d15 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -66,5 +66,10 @@ process GATK4_CNNSCOREVARIANTS { """ echo "" | gzip -c > ${prefix}.cnn.vcf.gz touch ${prefix}.cnn.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test new file mode 100644 index 00000000000..9795fbccf94 --- /dev/null +++ b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test @@ -0,0 +1,77 @@ +nextflow_process { + + name "Test Process GATK4_CNNSCOREVARIANTS" + script "../main.nf" + process "GATK4_CNNSCOREVARIANTS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/cnnscorevariants" + + test("homo sapiens - vcf") { + when { + process { + """ + input_vcf = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), + [], + [] + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + input = [input_vcf, fasta, fai, dict, [], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + ).match() } + ) + } + + } + + test("homo sapiens - vcf - stub") { + + options "-stub" + + when { + process { + """ + input_vcf = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), + [], + [] + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + input = [input_vcf, fasta, fai, dict, [], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap new file mode 100644 index 00000000000..b10467adfc0 --- /dev/null +++ b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap @@ -0,0 +1,65 @@ +{ + "homo sapiens - vcf": { + "content": [ + [ + "versions.yml:md5,7e0d98246eb35725469a53e6fb8acfbf" + ], + "test.cnn.vcf.gz", + "test.cnn.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:03:31.465934966" + }, + "homo sapiens - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.cnn.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.cnn.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,7e0d98246eb35725469a53e6fb8acfbf" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.cnn.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.cnn.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,7e0d98246eb35725469a53e6fb8acfbf" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:46:55.099673108" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md deleted file mode 100644 index c6a4545655a..00000000000 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml new file mode 100644 index 00000000000..e93eac37506 --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index 73d4a715877..cdb4b8f882d 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -2,8 +2,10 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(calls), path(model), path(ploidy) @@ -18,10 +20,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def calls_command = calls ? calls.collect{"--calls-shard-path $it"}.join(' ') : "" @@ -42,6 +40,7 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { $calls_command \\ $model_command \\ $ploidy_command \\ + $args \\ --output-genotyped-intervals ${prefix}_genotyped_intervals.vcf.gz \\ --output-genotyped-segments ${prefix}_genotyped_segments.vcf.gz \\ --output-denoised-copy-ratios ${prefix}_denoised.vcf.gz @@ -53,10 +52,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." - } def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_genotyped_intervals.vcf.gz diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test new file mode 100644 index 00000000000..f422027b50e --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -0,0 +1,140 @@ +nextflow_process { + + name "Test Process GATK4_POSTPROCESSGERMLINECNVCALLS" + script "../main.nf" + config "./nextflow.config" + process "GATK4_POSTPROCESSGERMLINECNVCALLS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/postprocessgermlinecnvcalls" + + setup { + run("GATK4_BEDTOINTERVALLIST") { + script "../../bedtointervallist/main.nf" + process { + """ + intervals = [[ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)] + dict = [ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] + + input = [intervals, dict] + """ + } + } + run("GATK4_COLLECTREADCOUNTS"){ + script "../../collectreadcounts/main.nf" + process { + """ + input_bam = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true), + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + ]) + + fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() + fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() + dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() + + input = [input_bam, fasta, fai, dict] + """ + } + } + run("GATK4_DETERMINEGERMLINECONTIGPLOIDY", alias: "GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT") { + script "../../determinegermlinecontigploidy/main.nf" + process { + """ + bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) + input = [ + GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[], tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), + [[],[]], + file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) + ] + """ + } + } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_COHORT") { + script "../../germlinecnvcaller/main.nf" + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[], tsv ]}) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]}) + """ + } + } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_CASE") { + script "../../germlinecnvcaller/main.nf" + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .first() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .map({ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]}) + """ + } + } + } + + test("homo sapiens - counts") { + + when { + process { + """ + input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - counts - stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap new file mode 100644 index 00000000000..7b70c6eb946 --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap @@ -0,0 +1,102 @@ +{ + "homo sapiens - counts - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_genotyped_intervals.vcf.gz" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_genotyped_segments.vcf.gz" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_denoised.vcf.gz" + ] + ], + "3": [ + "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" + ], + "denoised": [ + [ + { + "id": "test" + }, + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_denoised.vcf.gz" + ] + ], + "intervals": [ + [ + { + "id": "test" + }, + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_genotyped_intervals.vcf.gz" + ] + ], + "segments": [ + [ + { + "id": "test" + }, + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_genotyped_segments.vcf.gz" + ] + ], + "versions": [ + "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:38:04.517470815" + }, + "homo sapiens - counts": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + + ], + "denoised": [ + + ], + "intervals": [ + + ], + "segments": [ + + ], + "versions": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:32:42.388886811" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config similarity index 82% rename from tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config rename to modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config index 00adcaaa6bd..81566d90efa 100644 --- a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config @@ -1,22 +1,15 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'GATK4_COLLECTREADCOUNTS*' { ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" } - withName: 'GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT' { ext.args = "--interval-merging-rule OVERLAPPING_ONLY" ext.prefix = "ploidy" } - withName: 'GATK4_GERMLINECNVCALLER_COHORT' { ext.args = "--interval-merging-rule OVERLAPPING_ONLY --run-mode COHORT" } - withName: 'GATK4_GERMLINECNVCALLER_CASE' { ext.args = "--run-mode CASE" } - } diff --git a/modules/nf-core/gatk4spark/applybqsr/environment.yml b/modules/nf-core/gatk4spark/applybqsr/environment.yml index 14075a574ac..d3e954cdacc 100644 --- a/modules/nf-core/gatk4spark/applybqsr/environment.yml +++ b/modules/nf-core/gatk4spark/applybqsr/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4-spark=4.5.0.0 + - bioconda::gatk4-spark=4.6.1.0 diff --git a/modules/nf-core/gatk4spark/applybqsr/main.nf b/modules/nf-core/gatk4spark/applybqsr/main.nf index 316ddc0b1dd..5cc5c9c4a27 100644 --- a/modules/nf-core/gatk4spark/applybqsr/main.nf +++ b/modules/nf-core/gatk4spark/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4SPARK_APPLYBQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.5.0.0--hdfd78af_0': - 'biocontainers/gatk4-spark:4.5.0.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap index c4171be861f..db160a01fb6 100644 --- a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ], "bam": [ [ @@ -38,15 +38,15 @@ ] ], "versions": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T10:12:13.226593047" + "timestamp": "2024-11-06T11:47:37.292174976" }, "sarscov2 - cram": { "content": [ @@ -63,7 +63,7 @@ ] ], "2": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ], "bam": [ @@ -77,15 +77,15 @@ ] ], "versions": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:43:27.971279286" + "timestamp": "2024-11-06T11:48:24.575560544" }, "sarscov2 - bam": { "content": [ @@ -102,7 +102,7 @@ ], "2": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ], "bam": [ [ @@ -116,15 +116,15 @@ ], "versions": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:40:33.915518205" + "timestamp": "2024-11-06T11:46:46.042894548" }, "sarscov2 - bam intervals": { "content": [ @@ -141,7 +141,7 @@ ], "2": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ], "bam": [ [ @@ -155,14 +155,14 @@ ], "versions": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:42:52.310003463" + "timestamp": "2024-11-06T11:47:13.436442722" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml index 14075a574ac..d3e954cdacc 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4-spark=4.5.0.0 + - bioconda::gatk4-spark=4.6.1.0 diff --git a/modules/nf-core/gatk4spark/baserecalibrator/main.nf b/modules/nf-core/gatk4spark/baserecalibrator/main.nf index 32af761912f..304b1bc5240 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4spark/baserecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4SPARK_BASERECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.5.0.0--hdfd78af_0': - 'biocontainers/gatk4-spark:4.5.0.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) @@ -51,4 +51,16 @@ process GATK4SPARK_BASERECALIBRATOR { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.table + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test new file mode 100644 index 00000000000..ff6867d2f24 --- /dev/null +++ b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test @@ -0,0 +1,160 @@ +nextflow_process { + + name "Test Process GATK4SPARK_BASERECALIBRATOR" + script "../main.nf" + config "./nextflow.config" + process "GATK4SPARK_BASERECALIBRATOR" + + tag "modules" + tag "modules_nfcore" + tag "gatk4spark" + tag "gatk4spark/baserecalibrator" + + test("sarscov2 - bam") { + when { + process { + """ + input_bam = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + + input = [input_bam, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - cram") { + when { + process { + """ + input_cram = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + sites = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true) + sites_tbi = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + + input = [input_cram, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - intervals") { + when { + process { + """ + input_bam = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + + input = [input_bam, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - multi sites") { + when { + process { + """ + input_bam = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + sites = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)] + sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)] + input = [input_bam, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input_bam = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + + input = [input_bam, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap new file mode 100644 index 00000000000..c02ce4b1c8e --- /dev/null +++ b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap @@ -0,0 +1,167 @@ +{ + "sarscov2 - bam - multi sites": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:52:50.311106222" + }, + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:38:35.054385124" + }, + "homo sapiens - cram": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,ab82f81e027d8762b01c631b4ef792c0" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,ab82f81e027d8762b01c631b4ef792c0" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T12:03:12.23567219" + }, + "sarscov2 - bam - intervals": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,9ecb5f00a2229291705addc09c0ec231" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,9ecb5f00a2229291705addc09c0ec231" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:51:34.077518575" + }, + "sarscov2 - bam": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:49:36.893419883" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4spark/baserecalibrator/tests/nextflow.config b/modules/nf-core/gatk4spark/baserecalibrator/tests/nextflow.config new file mode 100644 index 00000000000..a1a17be887d --- /dev/null +++ b/modules/nf-core/gatk4spark/baserecalibrator/tests/nextflow.config @@ -0,0 +1,2 @@ +docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' + diff --git a/modules/nf-core/gatk4spark/markduplicates/environment.yml b/modules/nf-core/gatk4spark/markduplicates/environment.yml index 14075a574ac..d3e954cdacc 100644 --- a/modules/nf-core/gatk4spark/markduplicates/environment.yml +++ b/modules/nf-core/gatk4spark/markduplicates/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4-spark=4.5.0.0 + - bioconda::gatk4-spark=4.6.1.0 diff --git a/modules/nf-core/gatk4spark/markduplicates/main.nf b/modules/nf-core/gatk4spark/markduplicates/main.nf index b6a6daffea4..9cb74c8b363 100644 --- a/modules/nf-core/gatk4spark/markduplicates/main.nf +++ b/modules/nf-core/gatk4spark/markduplicates/main.nf @@ -4,8 +4,8 @@ process GATK4SPARK_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.5.0.0--hdfd78af_0': - 'biocontainers/gatk4-spark:4.5.0.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap index 4968a1ce650..f9366caead2 100644 --- a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap @@ -24,7 +24,7 @@ ], "3": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ], "bam_index": [ [ @@ -48,15 +48,15 @@ ] ], "versions": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:53:11.621016088" + "timestamp": "2024-11-06T11:52:48.84070018" }, "homo_sapiens - bam - metrics - output": { "content": [ @@ -95,7 +95,7 @@ ], "3": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ], "bam_index": [ @@ -113,27 +113,27 @@ ] ], "versions": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:53:53.339811107" + "timestamp": "2024-11-06T11:54:09.554533288" }, "homo_sapiens - bam - metrics - versions": { "content": [ [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:53:32.199010065" + "timestamp": "2024-11-06T11:53:39.648663125" }, "homo_sapiens - bam - metrics - bam_index": { "content": [ @@ -184,7 +184,7 @@ ] ], "3": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ], "bam_index": [ [ @@ -214,15 +214,15 @@ ] ], "versions": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T10:56:48.15652292" + "timestamp": "2024-11-06T11:54:21.987287007" }, "sarscov2 - bam": { "content": [ @@ -249,7 +249,7 @@ ], "3": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ], "bam_index": [ [ @@ -273,14 +273,14 @@ ] ], "versions": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:52:51.5386181" + "timestamp": "2024-11-06T11:51:28.270175346" } } \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index baf287515d1..6a9f2089be0 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -197,18 +197,9 @@ gangstr: gatk/indelrealigner: - modules/nf-core/gatk/indelrealigner/** - tests/modules/nf-core/gatk/indelrealigner/** -gatk4/cnnscorevariants: - - modules/nf-core/gatk4/cnnscorevariants/** - - tests/modules/nf-core/gatk4/cnnscorevariants/** -gatk4/postprocessgermlinecnvcalls: - - modules/nf-core/gatk4/postprocessgermlinecnvcalls/** - - tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/** gatk4/selectsamples: - modules/nf-core/gatk4/selectsamples/** - tests/modules/nf-core/gatk4/selectsamples/** -gatk4spark/baserecalibrator: - - modules/nf-core/gatk4spark/baserecalibrator/** - - tests/modules/nf-core/gatk4spark/baserecalibrator/** gem2/gem2bedmappability: - modules/nf-core/gem2/gem2bedmappability/** - tests/modules/nf-core/gem2/gem2bedmappability/** diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf b/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf deleted file mode 100644 index 8a218e1b884..00000000000 --- a/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_CNNSCOREVARIANTS } from '../../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' - -workflow test_gatk4_cnnscorevariants { - - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - [], - [] - ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - GATK4_CNNSCOREVARIANTS ( input, fasta, fai, dict, [], [] ) -} diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config b/tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/test.yml b/tests/modules/nf-core/gatk4/cnnscorevariants/test.yml deleted file mode 100644 index c26b9eab72d..00000000000 --- a/tests/modules/nf-core/gatk4/cnnscorevariants/test.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: gatk4 cnnscorevariants test_gatk4_cnnscorevariants - command: nextflow run ./tests/modules/nf-core/gatk4/cnnscorevariants -entry test_gatk4_cnnscorevariants -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config - tags: - - gatk4/cnnscorevariants - - gatk4 - files: - - path: output/gatk4/test.cnn.vcf.gz - contains: ["##ALT= [ [id:'test'], tsv ] }) - .groupTuple() - .combine(bed) - .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), - [[],[]], - contig_ploidy_table - ) - -// - intervals = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) - ] - GATK4_BEDTOINTERVALLIST ( intervals, dict ) -// - gcnvc_cohort_input = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ]}) - .groupTuple() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) - .map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]}) - - GATK4_GERMLINECNVCALLER_COHORT ( gcnvc_cohort_input ) - - gcnvc_case_input = GATK4_COLLECTREADCOUNTS.out.tsv - .first() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .map({ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]}) - GATK4_GERMLINECNVCALLER_CASE ( gcnvc_case_input ) - - GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .map({ meta, calls, meta2, model, meta3, ploidy -> [ [id:'test'], calls, model, ploidy ]}) - .set {postproc_in_cohort} - - GATK4_POSTPROCESSGERMLINECNVCALLS_COHORT ( postproc_in_cohort ) - - GATK4_GERMLINECNVCALLER_CASE.out.casecalls - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .map({ meta, calls, meta2, model, meta3, ploidy -> [ [id:'test'], calls, model, ploidy ]}) - .set {postproc_in_calls} - - GATK4_POSTPROCESSGERMLINECNVCALLS_CASE ( postproc_in_calls ) - -} diff --git a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/test.yml b/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/test.yml deleted file mode 100644 index 8ffb86ad0f9..00000000000 --- a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/test.yml +++ /dev/null @@ -1,21 +0,0 @@ -- name: gatk4 postprocessgermlinecnvcalls test_gatk4_postprocessgermlinecnvcalls - command: nextflow run ./tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls -entry test_gatk4_postprocessgermlinecnvcalls -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config - tags: - - gatk4/postprocessgermlinecnvcalls - - gatk4 - files: - - path: output/gatk4/test_denoised.vcf.gz - - path: output/gatk4/test_genotyped_intervals.vcf.gz - - path: output/gatk4/test_genotyped_segments.vcf.gz - - path: output/gatk4/versions.yml - -- name: gatk4 postprocessgermlinecnvcalls test_gatk4_postprocessgermlinecnvcalls stub - command: nextflow run ./tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls -entry test_gatk4_postprocessgermlinecnvcalls -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config -stub - tags: - - gatk4/postprocessgermlinecnvcalls - - gatk4 - files: - - path: output/gatk4/test_denoised.vcf.gz - - path: output/gatk4/test_genotyped_intervals.vcf.gz - - path: output/gatk4/test_genotyped_segments.vcf.gz - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4spark/baserecalibrator/main.nf b/tests/modules/nf-core/gatk4spark/baserecalibrator/main.nf deleted file mode 100644 index 79d5bbeeea2..00000000000 --- a/tests/modules/nf-core/gatk4spark/baserecalibrator/main.nf +++ /dev/null @@ -1,69 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4SPARK_BASERECALIBRATOR } from '../../../../../modules/nf-core/gatk4spark/baserecalibrator/main.nf' - -workflow test_gatk4spark_baserecalibrator { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - [] - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) - - GATK4SPARK_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi ) -} - -workflow test_gatk4spark_baserecalibrator_cram { - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - [] - ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) - sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) - - GATK4SPARK_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi ) -} - -workflow test_gatk4spark_baserecalibrator_intervals { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) - - GATK4SPARK_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi ) -} - -workflow test_gatk4spark_baserecalibrator_multiple_sites { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - [] - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - sites = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - ] - sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - ] - - GATK4SPARK_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi ) -} diff --git a/tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config b/tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/gatk4spark/baserecalibrator/test.yml b/tests/modules/nf-core/gatk4spark/baserecalibrator/test.yml deleted file mode 100644 index 61bebf2725d..00000000000 --- a/tests/modules/nf-core/gatk4spark/baserecalibrator/test.yml +++ /dev/null @@ -1,39 +0,0 @@ -- name: gatk4spark baserecalibrator test_gatk4spark_baserecalibrator - command: nextflow run ./tests/modules/nf-core/gatk4spark/baserecalibrator -entry test_gatk4spark_baserecalibrator -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config - tags: - - gatk4spark - - gatk4spark/baserecalibrator - files: - - path: output/gatk4spark/test.table - md5sum: e2e43abdc0c943c1a54dae816d0b9ea7 - - path: output/gatk4spark/versions.yml - -- name: gatk4spark baserecalibrator test_gatk4spark_baserecalibrator_cram - command: nextflow run ./tests/modules/nf-core/gatk4spark/baserecalibrator -entry test_gatk4spark_baserecalibrator_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config - tags: - - gatk4spark - - gatk4spark/baserecalibrator - files: - - path: output/gatk4spark/test.table - md5sum: 35d89a3811aa31711fc9815b6b80e6ec - - path: output/gatk4spark/versions.yml - -- name: gatk4spark baserecalibrator test_gatk4spark_baserecalibrator_intervals - command: nextflow run ./tests/modules/nf-core/gatk4spark/baserecalibrator -entry test_gatk4spark_baserecalibrator_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config - tags: - - gatk4spark - - gatk4spark/baserecalibrator - files: - - path: output/gatk4spark/test.table - md5sum: 9ecb5f00a2229291705addc09c0ec231 - - path: output/gatk4spark/versions.yml - -- name: gatk4spark baserecalibrator test_gatk4spark_baserecalibrator_multiple_sites - command: nextflow run ./tests/modules/nf-core/gatk4spark/baserecalibrator -entry test_gatk4spark_baserecalibrator_multiple_sites -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config - tags: - - gatk4spark - - gatk4spark/baserecalibrator - files: - - path: output/gatk4spark/test.table - md5sum: e2e43abdc0c943c1a54dae816d0b9ea7 - - path: output/gatk4spark/versions.yml From 431bc611b6f886cc1c04803eab14295361fb968c Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 07:56:58 +0000 Subject: [PATCH 17/59] fix sitedepthtobaf --- .../gatk4/sitedepthtobaf/tests/main.nf.test | 13 ++- .../sitedepthtobaf/tests/main.nf.test.snap | 94 +++---------------- 2 files changed, 23 insertions(+), 84 deletions(-) diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test index ce0c13a1bf7..8d077212605 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test @@ -8,6 +8,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "gatk4" + tag "gatk4/collectsvevidence" tag "gatk4/sitedepthtobaf" setup { @@ -66,7 +67,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.baf[0][1]).name, + file(process.out.baf_tbi[0][1]).name + ).match() } ) } @@ -98,7 +103,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.baf[0][1]).name, + file(process.out.baf_tbi[0][1]).name + ).match() } ) } diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap index 22fe5bcb99d..0c697cead8f 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap @@ -1,100 +1,30 @@ { "homo sapiens - bam - vcf - stub": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.baf.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.baf.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" - ], - "baf": [ - [ - { - "id": "test" - }, - "test.baf.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "baf_tbi": [ - [ - { - "id": "test" - }, - "test.baf.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" - ] - } + [ + "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" + ], + "test.baf.txt.gz", + "test.baf.txt.gz.tbi" ], "meta": { "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-05T09:08:59.446700288" + "timestamp": "2024-11-07T07:56:28.729680029" }, "homo sapiens - bam - vcf": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.baf.txt.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.baf.txt.gz.tbi:md5,2f146ddadfd39ca5f1f2fd79f727d427" - ] - ], - "2": [ - "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" - ], - "baf": [ - [ - { - "id": "test" - }, - "test.baf.txt.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "baf_tbi": [ - [ - { - "id": "test" - }, - "test.baf.txt.gz.tbi:md5,2f146ddadfd39ca5f1f2fd79f727d427" - ] - ], - "versions": [ - "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" - ] - } + [ + "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" + ], + "test.baf.txt.gz", + "test.baf.txt.gz.tbi" ], "meta": { "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-05T08:48:36.38848192" + "timestamp": "2024-11-07T07:55:58.514280421" } } \ No newline at end of file From e8525654228c9d92774eaeeb82a8d217dbe6271a Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 08:23:14 +0000 Subject: [PATCH 18/59] fix germlinecnvcaller --- .../germlinecnvcaller/tests/main.nf.test | 12 +- .../germlinecnvcaller/tests/main.nf.test.snap | 114 ++++++++++++++++++ 2 files changed, 121 insertions(+), 5 deletions(-) create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index c8a713214ed..b3955525c58 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -9,6 +9,8 @@ nextflow_process { tag "modules_nfcore" tag "gatk4" tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + tag "gatk4/bedtointervallist" tag "gatk4/germlinecnvcaller" setup { @@ -40,7 +42,7 @@ nextflow_process { script "../../determinegermlinecontigploidy/main.nf" process { """ - bed = file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists:true) input[0] = GATK4_COLLECTREADCOUNTS.out.tsv @@ -57,7 +59,7 @@ nextflow_process { script "../../bedtointervallist/main.nf" process { """ - input[0] = Channel.of([ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) + input[0] = Channel.of([[ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)]) input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]) """ } @@ -69,7 +71,7 @@ nextflow_process { process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [[:] , tsv ]}) + .map({ meta, tsv -> [[:], tsv ]}) .groupTuple() .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) @@ -95,9 +97,9 @@ nextflow_process { process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ , tsv ]}) + .map({ meta, tsv -> [[:], tsv ]}) .groupTuple() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) .map{ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]} """ diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap new file mode 100644 index 00000000000..e3d03986fa4 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -0,0 +1,114 @@ +{ + "homo sapiens - bam": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + + ], + "casecalls": [ + + ], + "cohortcalls": [ + + ], + "cohortmodel": [ + + ], + "versions": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T08:05:11.198859438" + }, + "homo sapiens - bam - stub": { + "content": [ + { + "0": [ + [ + { + + }, + [ + + ] + ] + ], + "1": [ + [ + { + + }, + [ + + ] + ] + ], + "2": [ + [ + { + + }, + [ + + ] + ] + ], + "3": [ + "versions.yml:md5,73418764ce886774da2a240630f45aff" + ], + "casecalls": [ + [ + { + + }, + [ + + ] + ] + ], + "cohortcalls": [ + [ + { + + }, + [ + + ] + ] + ], + "cohortmodel": [ + [ + { + + }, + [ + + ] + ] + ], + "versions": [ + "versions.yml:md5,73418764ce886774da2a240630f45aff" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T08:20:46.16021075" + } +} \ No newline at end of file From 35f82f1ebb7d5050875d22d970b4458b38086649 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 08:25:03 +0000 Subject: [PATCH 19/59] fix postprocessgermlinecnvcalls linting --- .../gatk4/postprocessgermlinecnvcalls/tests/main.nf.test | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test index f422027b50e..8d4bf4fa16c 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -8,6 +8,10 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "gatk4" + tag "gatk4/bedtointervallist" + tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + tag "gatk4/germlinecnvcaller" tag "gatk4/postprocessgermlinecnvcalls" setup { From a742d17d29c232f6cabd67e5ed0f7eb0b9ce2d2e Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 08:31:11 +0000 Subject: [PATCH 20/59] fix mergevcfs linting --- .../gatk4/mergevcfs/tests/main.nf.test | 3 +++ .../gatk4/mergevcfs/tests/main.nf.test.snap | 27 ++++++++++++------- 2 files changed, 21 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test index 77ace10a21b..343fff68c97 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.versions, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs") @@ -48,6 +49,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.versions, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs_no_dict") @@ -75,6 +77,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.versions, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs_no_dict_stub") diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap index 62cceed57bf..5fab6dca1ba 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap @@ -1,35 +1,44 @@ { "test_gatk4_mergevcfs_no_dict_stub": { "content": [ + [ + "versions.yml:md5,829a91432cc945f3227b1355587d25e0" + ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-14T14:57:40.784590995" + "timestamp": "2024-11-07T08:29:25.813956308" }, "test_gatk4_mergevcfs": { "content": [ + [ + "versions.yml:md5,829a91432cc945f3227b1355587d25e0" + ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-14T14:56:42.178255913" + "timestamp": "2024-11-07T08:28:42.580265083" }, "test_gatk4_mergevcfs_no_dict": { "content": [ + [ + "versions.yml:md5,829a91432cc945f3227b1355587d25e0" + ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-14T14:57:11.404322124" + "timestamp": "2024-11-07T08:29:12.795329336" } } \ No newline at end of file From 311a40d95b65c94d8f145f448253dcb8e0dbb381 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 08:38:25 +0000 Subject: [PATCH 21/59] revert biocontainer for determinegermlinecontigploidy --- .../gatk4/determinegermlinecontigploidy/main.nf | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index c4183bdd5bd..95fd05b79b7 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -3,10 +3,8 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { tag "$meta.id" label 'process_single' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 + container "nf-core/gatk:4.6.1.0" //Biocontainers is missing a package input: tuple val(meta), path(counts), path(bed), path(exclude_beds) @@ -22,6 +20,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def intervals = bed ? "--intervals ${bed}" : "" @@ -60,6 +62,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { """ stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + } prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}-calls From 2b0b3dfda1b000e1bc03e7c730e5f01af166c803 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 10:14:07 +0000 Subject: [PATCH 22/59] linting --- modules/nf-core/gatk4/asereadcounter/main.nf | 1 - modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 1 - modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf | 2 +- 3 files changed, 1 insertion(+), 3 deletions(-) diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf b/modules/nf-core/gatk4/asereadcounter/main.nf index 87cd0cce29f..93a3447538d 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf +++ b/modules/nf-core/gatk4/asereadcounter/main.nf @@ -53,7 +53,6 @@ process GATK4_ASEREADCOUNTER { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index b35412dce68..5213951d6f7 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -47,7 +47,6 @@ process GATK4_CREATESOMATICPANELOFNORMALS { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ echo "${prefix}" | gzip -c > ${prefix}.vcf.gz diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index 95fd05b79b7..1ddb57b2a2f 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -4,7 +4,7 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { label 'process_single' //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.6.1.0" //Biocontainers is missing a package + container "nf-core/gatk:4.6.1.0" //Biocontainers is missing a package input: tuple val(meta), path(counts), path(bed), path(exclude_beds) From 3f4f2b85610c8c149b008795c7f253be163c4def Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 10:14:51 +0000 Subject: [PATCH 23/59] fix estimatelibrarycomplexity tests --- .../nf-core/gatk4/estimatelibrarycomplexity/main.nf | 12 ++++++++++++ .../estimatelibrarycomplexity/tests/main.nf.test | 2 +- .../tests/main.nf.test.snap | 10 +++++----- 3 files changed, 18 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 31430a94291..33eda1ef59f 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -46,4 +46,16 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.metrics + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test index e23b65573c9..8552ca47dc2 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test @@ -75,7 +75,7 @@ nextflow_process { } - test("sarscov2 - bam - stub") { + test("homo sapiens - bam - stub") { options "-stub" diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap index fa478ca8f7a..73752535e93 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap @@ -12,18 +12,18 @@ }, "timestamp": "2024-10-31T11:01:20.304274717" }, - "sarscov2 - bam - stub": { + "homo sapiens - bam - stub": { "content": [ "test.metrics", [ - "versions.yml:md5,1d9c175d88b6c50c7dc999c1f70261a8" + "versions.yml:md5,a7b6a9d538151a577da5f5727ace31e6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T14:27:55.337569" + "timestamp": "2024-11-07T10:17:35.145738139" }, "homo_sapiens - bam": { "content": [ From de72bf8edd7173200176ab199cfc3cb5b2898daa Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 10:36:27 +0000 Subject: [PATCH 24/59] fix splitncigarreads tests --- modules/nf-core/gatk4/splitncigarreads/main.nf | 13 +++++++++++++ .../gatk4/splitncigarreads/tests/main.nf.test.snap | 8 ++++---- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index b5552391ea4..038613d06b7 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -46,4 +46,17 @@ process GATK4_SPLITNCIGARREADS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + } diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap index 86bccddb06b..5c2fee14781 100644 --- a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap @@ -16,14 +16,14 @@ "content": [ "test.bam", [ - "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb" + "versions.yml:md5,7ddd35e618d7a827231e7dc94f7a7b4e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:29:53.2252" + "timestamp": "2024-11-07T10:35:24.483631375" }, "test_gatk4_splitncigarreads": { "content": [ From caeecf1776641991a5aa95a8de4dc6f25452e83d Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 10:36:34 +0000 Subject: [PATCH 25/59] linting --- modules/nf-core/gatk4/splitcram/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/nf-core/gatk4/splitcram/main.nf b/modules/nf-core/gatk4/splitcram/main.nf index 48544298ab8..5fd623b7601 100644 --- a/modules/nf-core/gatk4/splitcram/main.nf +++ b/modules/nf-core/gatk4/splitcram/main.nf @@ -42,7 +42,6 @@ process GATK4_SPLITCRAM { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 From 2732a1716cdc771e919a196e91dc3170cd0144db Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 10:46:29 +0000 Subject: [PATCH 26/59] set compiledir for pytorch --- modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf | 1 + modules/nf-core/gatk4/germlinecnvcaller/main.nf | 1 + modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf | 1 + 3 files changed, 3 insertions(+) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index 1ddb57b2a2f..f2eacec8132 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -40,6 +40,7 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { } """ export THEANO_FLAGS="base_compiledir=\$PWD" + export PYTENSOR_FLAGS="base_compiledir=\$PWD" export OMP_NUM_THREADS=${task.cpus} export MKL_NUM_THREADS=${task.cpus} diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index 36749493b7f..ebbf9bcdc97 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -36,6 +36,7 @@ process GATK4_GERMLINECNVCALLER { } """ export THEANO_FLAGS="base_compiledir=\$PWD" + export PYTENSOR_FLAGS="base_compiledir=\$PWD" export OMP_NUM_THREADS=${task.cpus} export MKL_NUM_THREADS=${task.cpus} diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index cdb4b8f882d..e43aafe7fe8 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -34,6 +34,7 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { } """ export THEANO_FLAGS="base_compiledir=\$PWD" + export PYTENSOR_FLAGS="base_compiledir=\$PWD" gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ PostprocessGermlineCNVCalls \\ From 6bd2cf01712b940f4a1ec6349611b80153c38ba2 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 13:09:14 +0000 Subject: [PATCH 27/59] linting --- modules/nf-core/gatk4/variantstotable/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/gatk4/variantstotable/main.nf b/modules/nf-core/gatk4/variantstotable/main.nf index b61040aac48..34ef5a16866 100644 --- a/modules/nf-core/gatk4/variantstotable/main.nf +++ b/modules/nf-core/gatk4/variantstotable/main.nf @@ -8,7 +8,7 @@ process GATK4_VARIANTSTOTABLE { 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: - tuple val(meta), path(vcf), path(tbi), path(arguments_file), path(include_intervals), path(exclude_intervals) + tuple val(meta), path(vcf), path(tbi), path(arguments_file), path(include_intervals), path(exclude_intervals) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) tuple val(meta4), path(dict) @@ -42,8 +42,8 @@ process GATK4_VARIANTSTOTABLE { --reference $fasta \\ --tmp-dir . \\ $arguments_file_arg \\ - $include_intervals \\ - $exclude_intervals + $include_intervals_arg \\ + $exclude_intervals_arg cat <<-END_VERSIONS > versions.yml "${task.process}": From bb6eeb5e6990754ede9453cc999ebd0bc80457f5 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 13:17:54 +0000 Subject: [PATCH 28/59] linting --- modules/nf-core/gatk4/denoisereadcounts/main.nf | 1 - modules/nf-core/gatk4/printsvevidence/main.nf | 12 +++++++++--- .../gatk4/printsvevidence/tests/main.nf.test.snap | 10 +++++----- 3 files changed, 14 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/gatk4/denoisereadcounts/main.nf b/modules/nf-core/gatk4/denoisereadcounts/main.nf index 3d4637d8539..e142262cf1b 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/main.nf +++ b/modules/nf-core/gatk4/denoisereadcounts/main.nf @@ -46,7 +46,6 @@ process GATK4_DENOISEREADCOUNTS { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_standardizedCR.tsv diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index a303b535714..d49948ce567 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -65,10 +65,16 @@ process GATK4_PRINTSVEVIDENCE { """ stub: - prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" + def file_name = evidence_files[0].getFileName() + def file_type = file_name =~ ".sr.txt" ? "sr" : + file_name =~ ".pe.txt" ? "pe" : + file_name =~ ".baf.txt" ? "baf" : + file_name =~ ".rd.txt" ? "rd" : + false """ - echo "" | gzip -c > printed_evidence.txt.gz - touch printed_evidence.txt.gz.tbi + echo "" | gzip -c > ${prefix}.${file_type}.txt.gz + touch ${prefix}.${file_type}.txt.gz.tbi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap index aff2e29ad80..18c153e8b9d 100644 --- a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap @@ -85,7 +85,7 @@ [ ], - "printed_evidence.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "[].pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -93,7 +93,7 @@ [ ], - "printed_evidence.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "[].pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -104,7 +104,7 @@ [ ], - "printed_evidence.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "[].pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "printed_evidence_index": [ @@ -112,7 +112,7 @@ [ ], - "printed_evidence.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "[].pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -124,6 +124,6 @@ "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-04T13:40:15.747273218" + "timestamp": "2024-11-07T13:15:03.047838982" } } \ No newline at end of file From b3a768cf0513d489f19b1b341e62d307eb30a1e1 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 13:37:27 +0000 Subject: [PATCH 29/59] fix container definition --- modules/nf-core/gatk4/germlinecnvcaller/main.nf | 14 ++++++++++---- .../gatk4/postprocessgermlinecnvcalls/main.nf | 14 ++++++++++---- 2 files changed, 20 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index ebbf9bcdc97..cf5c361ff3f 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -2,10 +2,8 @@ process GATK4_GERMLINECNVCALLER { tag "$meta.id" label 'process_single' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 + container "nf-core/gatk:4.6.1.0" //Biocontainers is missing a package input: tuple val(meta), path(tsv), path(intervals), path(ploidy), path(model) @@ -20,6 +18,10 @@ process GATK4_GERMLINECNVCALLER { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def intervals_command = intervals ? "--intervals ${intervals}" : "" @@ -57,6 +59,10 @@ process GATK4_GERMLINECNVCALLER { """ stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + } def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir -p ${prefix}-cnv-calls/${prefix}-calls diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index e43aafe7fe8..03c1d47946a 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -2,10 +2,8 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { tag "$meta.id" label 'process_single' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 + container "nf-core/gatk:4.6.1.0" //Biocontainers is missing a package input: tuple val(meta), path(calls), path(model), path(ploidy) @@ -20,6 +18,10 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def calls_command = calls ? calls.collect{"--calls-shard-path $it"}.join(' ') : "" @@ -53,6 +55,10 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { """ stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + } def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_genotyped_intervals.vcf.gz From e9c8f647e854fc05244d5b23ceb91cc04d494583 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 7 Nov 2024 20:56:31 +0000 Subject: [PATCH 30/59] are we there yet? --- .../tests/main.nf.test | 12 +- .../tests/main.nf.test.snap | 94 ++---------- .../nf-core/gatk4/germlinecnvcaller/main.nf | 4 +- .../germlinecnvcaller/tests/main.nf.test | 6 +- .../germlinecnvcaller/tests/main.nf.test.snap | 142 ++++++++++++++++-- .../gatk4/postprocessgermlinecnvcalls/main.nf | 6 +- .../tests/main.nf.test | 4 +- .../tests/main.nf.test.snap | 62 ++++++-- 8 files changed, 206 insertions(+), 124 deletions(-) diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test index d602b9c7688..1821a00fb66 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test @@ -43,7 +43,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + ).match() } ) } @@ -73,7 +77,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + ).match() } ) } diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap index 098b9852fe6..d4da4f2a7da 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap @@ -1,100 +1,30 @@ { "homo sapiens - genomicsdb": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.vcf.gz:md5,bd443afef3ba3aa5b7f5652313664e9e" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4" - ] - ], - "2": [ - "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" - ], - "tbi": [ - [ - { - "id": "test" - }, - "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4" - ] - ], - "vcf": [ - [ - { - "id": "test" - }, - "test.vcf.gz:md5,bd443afef3ba3aa5b7f5652313664e9e" - ] - ], - "versions": [ - "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" - ] - } + [ + "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" + ], + "test.vcf.gz", + "test.vcf.gz.tbi" ], "meta": { "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-04T11:37:41.734498184" + "timestamp": "2024-11-07T20:27:41.348681175" }, "homo sapiens - genomicsdb - stub": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.vcf.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" - ], - "tbi": [ - [ - { - "id": "test" - }, - "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "vcf": [ - [ - { - "id": "test" - }, - "test.vcf.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" - ] - ], - "versions": [ - "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" - ] - } + [ + "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" + ], + "test.vcf.gz", + "test.vcf.gz.tbi" ], "meta": { "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-04T11:37:55.969655125" + "timestamp": "2024-11-07T20:27:58.84258624" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index cf5c361ff3f..2a729f840db 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -20,7 +20,7 @@ process GATK4_GERMLINECNVCALLER { script: // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" @@ -61,7 +61,7 @@ process GATK4_GERMLINECNVCALLER { stub: // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." } def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index b3955525c58..e7d2e817609 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -46,7 +46,7 @@ nextflow_process { contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists:true) input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [[:], tsv ] }) + .map({ meta, tsv -> [[id:'test'], tsv ] }) .groupTuple() .combine(bed) .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) @@ -71,7 +71,7 @@ nextflow_process { process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [[:], tsv ]}) + .map({ meta, tsv -> [[id:'test'], tsv ] }) .groupTuple() .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) @@ -97,7 +97,7 @@ nextflow_process { process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [[:], tsv ]}) + .map({ meta, tsv -> [[id:'test'], tsv ] }) .groupTuple() .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap index e3d03986fa4..7a330e81489 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -3,28 +3,142 @@ "content": [ { "0": [ - + [ + { + "id": "test" + }, + [ + [ + "baseline_copy_number_t.tsv:md5,a8f848d75d241f7932ffdca261bffe7b", + "log_c_emission_tc.tsv:md5,02c49de9d58dc21fddeb54b4104f4aab", + "log_q_c_tc.tsv:md5,f6b3b721c503f5406e259f199202ba8c", + "mu_denoised_copy_ratio_t.tsv:md5,8a86b2c88558bae86bb7470f5f00e040", + "mu_psi_s_log__.tsv:md5,fe52c89b83d9c322c2758317235a9bb2", + "mu_read_depth_s_log__.tsv:md5,895d0d31e57004e5f54bdf1b1a3878ae", + "mu_z_su.tsv:md5,f012d75023113664cf03f0e28f41dc40", + "sample_name.txt:md5,5cf41871eea16c0fbfdcb7f0f664ed95", + "std_denoised_copy_ratio_t.tsv:md5,c283b818689b7260b437905e168e0ddb", + "std_psi_s_log__.tsv:md5,ce16b09818baa8da9a580cec33f38c26", + "std_read_depth_s_log__.tsv:md5,4a26cc55bf837f70c658f8e1142cf208", + "std_z_su.tsv:md5,7bc68a10eaec52f5a22d1386af90e2b0" + ], + [ + "baseline_copy_number_t.tsv:md5,51670372d61cf525a2303d293129fc2e", + "log_c_emission_tc.tsv:md5,c9153989adfad01a3f962c03c10cf30e", + "log_q_c_tc.tsv:md5,21bd7ce921286bc416968cce51994c0e", + "mu_denoised_copy_ratio_t.tsv:md5,d47e8bd17cf2f5226fccd369fd2e64b0", + "mu_psi_s_log__.tsv:md5,6d1677b6f7ec7b9538208257f717cc6c", + "mu_read_depth_s_log__.tsv:md5,63ca74e20d21f077f84c2171763512c2", + "mu_z_su.tsv:md5,90659ad8832da4573b7bca9b3146dd96", + "sample_name.txt:md5,640a474d6f73b01524287f50ca538c04", + "std_denoised_copy_ratio_t.tsv:md5,5dfd9d3a38168d6af585b101f0e62ac2", + "std_psi_s_log__.tsv:md5,728b9a2b239665fd68a35f79c6148c50", + "std_read_depth_s_log__.tsv:md5,1f4d0a529de41a661dbf54eb7fed1a93", + "std_z_su.tsv:md5,e3c5e3c96e79a80d234e80fc57734206" + ], + "calling_config.json:md5,dc78889e3d0ba1adf02d10db0194128e", + "denoising_config.json:md5,d2171570b7c746be4d2ce35d9b8db18c", + "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", + "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd" + ] + ] ], "1": [ - + [ + { + "id": "test" + }, + [ + "calling_config.json:md5,dc78889e3d0ba1adf02d10db0194128e", + "denoising_config.json:md5,d2171570b7c746be4d2ce35d9b8db18c", + "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", + "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd", + "log_q_tau_tk.tsv:md5,0b62b298d25aaa6183f2cc9918b94602", + "mu_W_tu.tsv:md5,d8c78c7a8182eb962f85f82b4a7d477e", + "mu_ard_u_interval__.tsv:md5,13e118b1a505a0c4164974c9dca8036f", + "mu_log_mean_bias_t.tsv:md5,353c41a99919004e377a43772cc430af", + "mu_psi_t_log__.tsv:md5,f776663188dc8b581e556f8a614b68b6", + "std_W_tu.tsv:md5,e075020d8faa4d69ea530a8cecbe75c2", + "std_ard_u_interval__.tsv:md5,151917e122b18c49adf3021409f1ccea", + "std_log_mean_bias_t.tsv:md5,d3257bbec6896549428b8b73f6d7b3a0", + "std_psi_t_log__.tsv:md5,0767d18a424d196aa5a596d03507bc0c" + ] + ] ], "2": [ ], "3": [ - + "versions.yml:md5,73418764ce886774da2a240630f45aff" ], "casecalls": [ ], "cohortcalls": [ - + [ + { + "id": "test" + }, + [ + [ + "baseline_copy_number_t.tsv:md5,a8f848d75d241f7932ffdca261bffe7b", + "log_c_emission_tc.tsv:md5,02c49de9d58dc21fddeb54b4104f4aab", + "log_q_c_tc.tsv:md5,f6b3b721c503f5406e259f199202ba8c", + "mu_denoised_copy_ratio_t.tsv:md5,8a86b2c88558bae86bb7470f5f00e040", + "mu_psi_s_log__.tsv:md5,fe52c89b83d9c322c2758317235a9bb2", + "mu_read_depth_s_log__.tsv:md5,895d0d31e57004e5f54bdf1b1a3878ae", + "mu_z_su.tsv:md5,f012d75023113664cf03f0e28f41dc40", + "sample_name.txt:md5,5cf41871eea16c0fbfdcb7f0f664ed95", + "std_denoised_copy_ratio_t.tsv:md5,c283b818689b7260b437905e168e0ddb", + "std_psi_s_log__.tsv:md5,ce16b09818baa8da9a580cec33f38c26", + "std_read_depth_s_log__.tsv:md5,4a26cc55bf837f70c658f8e1142cf208", + "std_z_su.tsv:md5,7bc68a10eaec52f5a22d1386af90e2b0" + ], + [ + "baseline_copy_number_t.tsv:md5,51670372d61cf525a2303d293129fc2e", + "log_c_emission_tc.tsv:md5,c9153989adfad01a3f962c03c10cf30e", + "log_q_c_tc.tsv:md5,21bd7ce921286bc416968cce51994c0e", + "mu_denoised_copy_ratio_t.tsv:md5,d47e8bd17cf2f5226fccd369fd2e64b0", + "mu_psi_s_log__.tsv:md5,6d1677b6f7ec7b9538208257f717cc6c", + "mu_read_depth_s_log__.tsv:md5,63ca74e20d21f077f84c2171763512c2", + "mu_z_su.tsv:md5,90659ad8832da4573b7bca9b3146dd96", + "sample_name.txt:md5,640a474d6f73b01524287f50ca538c04", + "std_denoised_copy_ratio_t.tsv:md5,5dfd9d3a38168d6af585b101f0e62ac2", + "std_psi_s_log__.tsv:md5,728b9a2b239665fd68a35f79c6148c50", + "std_read_depth_s_log__.tsv:md5,1f4d0a529de41a661dbf54eb7fed1a93", + "std_z_su.tsv:md5,e3c5e3c96e79a80d234e80fc57734206" + ], + "calling_config.json:md5,dc78889e3d0ba1adf02d10db0194128e", + "denoising_config.json:md5,d2171570b7c746be4d2ce35d9b8db18c", + "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", + "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd" + ] + ] ], "cohortmodel": [ - + [ + { + "id": "test" + }, + [ + "calling_config.json:md5,dc78889e3d0ba1adf02d10db0194128e", + "denoising_config.json:md5,d2171570b7c746be4d2ce35d9b8db18c", + "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", + "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd", + "log_q_tau_tk.tsv:md5,0b62b298d25aaa6183f2cc9918b94602", + "mu_W_tu.tsv:md5,d8c78c7a8182eb962f85f82b4a7d477e", + "mu_ard_u_interval__.tsv:md5,13e118b1a505a0c4164974c9dca8036f", + "mu_log_mean_bias_t.tsv:md5,353c41a99919004e377a43772cc430af", + "mu_psi_t_log__.tsv:md5,f776663188dc8b581e556f8a614b68b6", + "std_W_tu.tsv:md5,e075020d8faa4d69ea530a8cecbe75c2", + "std_ard_u_interval__.tsv:md5,151917e122b18c49adf3021409f1ccea", + "std_log_mean_bias_t.tsv:md5,d3257bbec6896549428b8b73f6d7b3a0", + "std_psi_t_log__.tsv:md5,0767d18a424d196aa5a596d03507bc0c" + ] + ] ], "versions": [ - + "versions.yml:md5,73418764ce886774da2a240630f45aff" ] } ], @@ -32,7 +146,7 @@ "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T08:05:11.198859438" + "timestamp": "2024-11-07T20:37:04.485536889" }, "homo sapiens - bam - stub": { "content": [ @@ -40,7 +154,7 @@ "0": [ [ { - + "id": "test" }, [ @@ -50,7 +164,7 @@ "1": [ [ { - + "id": "test" }, [ @@ -60,7 +174,7 @@ "2": [ [ { - + "id": "test" }, [ @@ -73,7 +187,7 @@ "casecalls": [ [ { - + "id": "test" }, [ @@ -83,7 +197,7 @@ "cohortcalls": [ [ { - + "id": "test" }, [ @@ -93,7 +207,7 @@ "cohortmodel": [ [ { - + "id": "test" }, [ @@ -109,6 +223,6 @@ "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T08:20:46.16021075" + "timestamp": "2024-11-07T20:37:29.536430707" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index 03c1d47946a..fa43dc7b559 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -20,7 +20,7 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { script: // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" @@ -30,7 +30,7 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK GermlineCNVCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + log.info '[GATK PostProcessGermlineCnvCalls] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = (task.memory.mega*0.8).intValue() } @@ -57,7 +57,7 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { stub: // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." + error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." } def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test index 8d4bf4fa16c..2f2b3a0ce25 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -58,7 +58,7 @@ nextflow_process { bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) input = [ GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [[], tsv ] }) + .map({ meta, tsv -> [[id:'test'], tsv ] }) .groupTuple() .combine(bed) .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), @@ -73,7 +73,7 @@ nextflow_process { process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [[], tsv ]}) + .map({ meta, tsv -> [[id:'test'], tsv ] }) .groupTuple() .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap index 7b70c6eb946..8803c886b0e 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_genotyped_intervals.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_genotyped_intervals.vcf.gz" ] ], "1": [ @@ -15,7 +15,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_genotyped_segments.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_genotyped_segments.vcf.gz" ] ], "2": [ @@ -23,7 +23,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_denoised.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_denoised.vcf.gz" ] ], "3": [ @@ -34,7 +34,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_denoised.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_denoised.vcf.gz" ] ], "intervals": [ @@ -42,7 +42,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_genotyped_intervals.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_genotyped_intervals.vcf.gz" ] ], "segments": [ @@ -50,7 +50,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/76/292b99badda423e764042bd95f853f/test_genotyped_segments.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_genotyped_segments.vcf.gz" ] ], "versions": [ @@ -62,34 +62,64 @@ "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-06T11:38:04.517470815" + "timestamp": "2024-11-07T20:54:43.223517721" }, "homo sapiens - counts": { "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test_genotyped_intervals.vcf.gz:md5,ae40ac5c4a04c95941406214fe0dc976" + ] ], "1": [ - + [ + { + "id": "test" + }, + "test_genotyped_segments.vcf.gz:md5,7d243ff2bccf292e72b3cf80d1f500fd" + ] ], "2": [ - + [ + { + "id": "test" + }, + "/workspace/nf-core-modules/.nf-test/tests/ed5726b677bb1f1830d5f6b92b099cb9/work/15/a70d5164a2f3c28a05f6a99c8ee8fe/test_denoised.vcf.gz" + ] ], "3": [ - + "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" ], "denoised": [ - + [ + { + "id": "test" + }, + "/workspace/nf-core-modules/.nf-test/tests/ed5726b677bb1f1830d5f6b92b099cb9/work/15/a70d5164a2f3c28a05f6a99c8ee8fe/test_denoised.vcf.gz" + ] ], "intervals": [ - + [ + { + "id": "test" + }, + "test_genotyped_intervals.vcf.gz:md5,ae40ac5c4a04c95941406214fe0dc976" + ] ], "segments": [ - + [ + { + "id": "test" + }, + "test_genotyped_segments.vcf.gz:md5,7d243ff2bccf292e72b3cf80d1f500fd" + ] ], "versions": [ - + "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" ] } ], @@ -97,6 +127,6 @@ "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-06T11:32:42.388886811" + "timestamp": "2024-11-07T20:54:14.534954616" } } \ No newline at end of file From dd223727669cbc22f7503e56399916b3b108fc9d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 7 Nov 2024 21:46:27 -0600 Subject: [PATCH 31/59] ci: Only run if the PR is from the main repo https://github.com/orgs/community/discussions/26829#discussioncomment-3253575 --- .github/workflows/wave.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml index 381c2240b36..e4d36ffcf99 100644 --- a/.github/workflows/wave.yml +++ b/.github/workflows/wave.yml @@ -16,8 +16,7 @@ jobs: generate-matrix: name: generate-matrix runs-on: ubuntu-latest - if: github.repository == 'nf-core/modules' - + if: ${{ github.event.pull_request.head.repo.full_name == github.repository }} steps: - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 From 3289c56bc7dcc81fd51006f3509cd6392151dce6 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Fri, 8 Nov 2024 08:57:54 +0000 Subject: [PATCH 32/59] apply yaml schema and renovate comments to environment.yml --- modules/nf-core/gatk4/addorreplacereadgroups/environment.yml | 5 ++++- modules/nf-core/gatk4/annotateintervals/environment.yml | 5 ++++- modules/nf-core/gatk4/applybqsr/environment.yml | 5 ++++- modules/nf-core/gatk4/applyvqsr/environment.yml | 5 ++++- modules/nf-core/gatk4/asereadcounter/environment.yml | 5 ++++- modules/nf-core/gatk4/baserecalibrator/environment.yml | 5 ++++- modules/nf-core/gatk4/bedtointervallist/environment.yml | 5 ++++- modules/nf-core/gatk4/calculatecontamination/environment.yml | 5 ++++- modules/nf-core/gatk4/calibratedragstrmodel/environment.yml | 5 ++++- modules/nf-core/gatk4/cnnscorevariants/environment.yml | 5 ++++- modules/nf-core/gatk4/collectreadcounts/environment.yml | 5 ++++- modules/nf-core/gatk4/collectsvevidence/environment.yml | 5 ++++- modules/nf-core/gatk4/combinegvcfs/environment.yml | 5 ++++- modules/nf-core/gatk4/composestrtablefile/environment.yml | 5 ++++- modules/nf-core/gatk4/condensedepthevidence/environment.yml | 5 ++++- .../gatk4/createreadcountpanelofnormals/environment.yml | 5 ++++- .../nf-core/gatk4/createsequencedictionary/environment.yml | 5 ++++- .../gatk4/createsomaticpanelofnormals/environment.yml | 5 ++++- modules/nf-core/gatk4/denoisereadcounts/environment.yml | 5 ++++- .../gatk4/determinegermlinecontigploidy/environment.yml | 5 ++++- .../nf-core/gatk4/estimatelibrarycomplexity/environment.yml | 5 ++++- modules/nf-core/gatk4/fastqtosam/environment.yml | 5 ++++- modules/nf-core/gatk4/filterintervals/environment.yml | 5 ++++- modules/nf-core/gatk4/filtermutectcalls/environment.yml | 5 ++++- modules/nf-core/gatk4/filtervarianttranches/environment.yml | 5 ++++- modules/nf-core/gatk4/gatherbqsrreports/environment.yml | 5 ++++- modules/nf-core/gatk4/gatherpileupsummaries/environment.yml | 5 ++++- modules/nf-core/gatk4/genomicsdbimport/environment.yml | 5 ++++- modules/nf-core/gatk4/genotypegvcfs/environment.yml | 5 ++++- modules/nf-core/gatk4/germlinecnvcaller/environment.yml | 5 ++++- modules/nf-core/gatk4/getpileupsummaries/environment.yml | 5 ++++- modules/nf-core/gatk4/haplotypecaller/environment.yml | 5 ++++- modules/nf-core/gatk4/indexfeaturefile/environment.yml | 5 ++++- modules/nf-core/gatk4/intervallisttobed/environment.yml | 5 ++++- modules/nf-core/gatk4/intervallisttools/environment.yml | 5 ++++- .../nf-core/gatk4/learnreadorientationmodel/environment.yml | 5 ++++- .../nf-core/gatk4/leftalignandtrimvariants/environment.yml | 5 ++++- modules/nf-core/gatk4/markduplicates/environment.yml | 5 ++++- modules/nf-core/gatk4/mergebamalignment/environment.yml | 5 ++++- modules/nf-core/gatk4/mergemutectstats/environment.yml | 5 ++++- modules/nf-core/gatk4/mergevcfs/environment.yml | 5 ++++- modules/nf-core/gatk4/mutect2/environment.yml | 5 ++++- .../gatk4/postprocessgermlinecnvcalls/environment.yml | 5 ++++- modules/nf-core/gatk4/preprocessintervals/environment.yml | 5 ++++- modules/nf-core/gatk4/printreads/environment.yml | 5 ++++- modules/nf-core/gatk4/printsvevidence/environment.yml | 5 ++++- modules/nf-core/gatk4/reblockgvcf/environment.yml | 5 ++++- modules/nf-core/gatk4/revertsam/environment.yml | 5 ++++- modules/nf-core/gatk4/samtofastq/environment.yml | 5 ++++- modules/nf-core/gatk4/selectvariants/environment.yml | 5 ++++- modules/nf-core/gatk4/shiftfasta/environment.yml | 5 ++++- modules/nf-core/gatk4/sitedepthtobaf/environment.yml | 5 ++++- modules/nf-core/gatk4/splitcram/environment.yml | 5 ++++- modules/nf-core/gatk4/splitintervals/environment.yml | 5 ++++- modules/nf-core/gatk4/splitncigarreads/environment.yml | 5 ++++- modules/nf-core/gatk4/svannotate/environment.yml | 5 ++++- modules/nf-core/gatk4/svcluster/environment.yml | 5 ++++- modules/nf-core/gatk4/variantfiltration/environment.yml | 5 ++++- modules/nf-core/gatk4/variantrecalibrator/environment.yml | 5 ++++- modules/nf-core/gatk4/variantstotable/environment.yml | 5 ++++- 60 files changed, 240 insertions(+), 60 deletions(-) diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/asereadcounter/environment.yml +++ b/modules/nf-core/gatk4/asereadcounter/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/cnnscorevariants/environment.yml b/modules/nf-core/gatk4/cnnscorevariants/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/environment.yml +++ b/modules/nf-core/gatk4/cnnscorevariants/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectsvevidence/environment.yml b/modules/nf-core/gatk4/collectsvevidence/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/collectsvevidence/environment.yml +++ b/modules/nf-core/gatk4/collectsvevidence/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/condensedepthevidence/environment.yml b/modules/nf-core/gatk4/condensedepthevidence/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/environment.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/fastqtosam/environment.yml b/modules/nf-core/gatk4/fastqtosam/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/fastqtosam/environment.yml +++ b/modules/nf-core/gatk4/fastqtosam/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 8a70182eac7..501478df17b 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -1,8 +1,11 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 - bioconda::htslib=1.19.1 - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printsvevidence/environment.yml b/modules/nf-core/gatk4/printsvevidence/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/printsvevidence/environment.yml +++ b/modules/nf-core/gatk4/printsvevidence/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/reblockgvcf/environment.yml b/modules/nf-core/gatk4/reblockgvcf/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/reblockgvcf/environment.yml +++ b/modules/nf-core/gatk4/reblockgvcf/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/selectvariants/environment.yml b/modules/nf-core/gatk4/selectvariants/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/selectvariants/environment.yml +++ b/modules/nf-core/gatk4/selectvariants/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/shiftfasta/environment.yml b/modules/nf-core/gatk4/shiftfasta/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/shiftfasta/environment.yml +++ b/modules/nf-core/gatk4/shiftfasta/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitcram/environment.yml b/modules/nf-core/gatk4/splitcram/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/splitcram/environment.yml +++ b/modules/nf-core/gatk4/splitcram/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/svannotate/environment.yml +++ b/modules/nf-core/gatk4/svannotate/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/svcluster/environment.yml +++ b/modules/nf-core/gatk4/svcluster/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index e93eac37506..fbeeb1eafc2 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantstotable/environment.yml b/modules/nf-core/gatk4/variantstotable/environment.yml index 03610def61e..7a5362b0171 100644 --- a/modules/nf-core/gatk4/variantstotable/environment.yml +++ b/modules/nf-core/gatk4/variantstotable/environment.yml @@ -1,6 +1,9 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gatk4 +  - bioconda::gatk4=4.6.1.0 From 39e2aaf5f484123c03862a38e70886a8de1909cd Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Fri, 8 Nov 2024 09:12:59 +0000 Subject: [PATCH 33/59] fix determinegermlinecontigploidy config --- .../tests/nextflow.config | 2 +- .../tests/main.nf.test.snap | 28 +++++++++---------- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config index c2455205820..2767daca231 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config @@ -2,7 +2,7 @@ process { withName: GATK4_COLLECTREADCOUNTS { ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" } - withName: GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT { + withName: GATK4_DETERMINEGERMLINECONTIGPLOIDY { ext.args = "--interval-merging-rule OVERLAPPING_ONLY" } } diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap index 8803c886b0e..7858d1e4bf3 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_genotyped_intervals.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_genotyped_intervals.vcf.gz" ] ], "1": [ @@ -15,7 +15,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_genotyped_segments.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_genotyped_segments.vcf.gz" ] ], "2": [ @@ -23,7 +23,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_denoised.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_denoised.vcf.gz" ] ], "3": [ @@ -34,7 +34,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_denoised.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_denoised.vcf.gz" ] ], "intervals": [ @@ -42,7 +42,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_genotyped_intervals.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_genotyped_intervals.vcf.gz" ] ], "segments": [ @@ -50,7 +50,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/d7/ae01e9ed375d03636fdda6500f7410/test_genotyped_segments.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_genotyped_segments.vcf.gz" ] ], "versions": [ @@ -62,7 +62,7 @@ "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T20:54:43.223517721" + "timestamp": "2024-11-08T09:09:36.05466689" }, "homo sapiens - counts": { "content": [ @@ -72,7 +72,7 @@ { "id": "test" }, - "test_genotyped_intervals.vcf.gz:md5,ae40ac5c4a04c95941406214fe0dc976" + "test_genotyped_intervals.vcf.gz:md5,16185817eecc1818566925612a17e22b" ] ], "1": [ @@ -80,7 +80,7 @@ { "id": "test" }, - "test_genotyped_segments.vcf.gz:md5,7d243ff2bccf292e72b3cf80d1f500fd" + "test_genotyped_segments.vcf.gz:md5,367d6c25a4e825df8e266a62933abf2d" ] ], "2": [ @@ -88,7 +88,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/ed5726b677bb1f1830d5f6b92b099cb9/work/15/a70d5164a2f3c28a05f6a99c8ee8fe/test_denoised.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/ed5726b677bb1f1830d5f6b92b099cb9/work/57/cfa7ba4c9e3d0425a8cdc02e703820/test_denoised.vcf.gz" ] ], "3": [ @@ -99,7 +99,7 @@ { "id": "test" }, - "/workspace/nf-core-modules/.nf-test/tests/ed5726b677bb1f1830d5f6b92b099cb9/work/15/a70d5164a2f3c28a05f6a99c8ee8fe/test_denoised.vcf.gz" + "/workspace/nf-core-modules/.nf-test/tests/ed5726b677bb1f1830d5f6b92b099cb9/work/57/cfa7ba4c9e3d0425a8cdc02e703820/test_denoised.vcf.gz" ] ], "intervals": [ @@ -107,7 +107,7 @@ { "id": "test" }, - "test_genotyped_intervals.vcf.gz:md5,ae40ac5c4a04c95941406214fe0dc976" + "test_genotyped_intervals.vcf.gz:md5,16185817eecc1818566925612a17e22b" ] ], "segments": [ @@ -115,7 +115,7 @@ { "id": "test" }, - "test_genotyped_segments.vcf.gz:md5,7d243ff2bccf292e72b3cf80d1f500fd" + "test_genotyped_segments.vcf.gz:md5,367d6c25a4e825df8e266a62933abf2d" ] ], "versions": [ @@ -127,6 +127,6 @@ "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T20:54:14.534954616" + "timestamp": "2024-11-08T09:08:53.062177092" } } \ No newline at end of file From dafbfe9479ee595f3803ca115a7c4a398262c189 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 8 Nov 2024 11:28:37 -0600 Subject: [PATCH 34/59] chore: Add renovate comments to bowtie2 for sanity check --- modules/nf-core/bowtie/align/environment.yml | 2 ++ modules/nf-core/bowtie2/align/environment.yml | 5 +++++ 2 files changed, 7 insertions(+) diff --git a/modules/nf-core/bowtie/align/environment.yml b/modules/nf-core/bowtie/align/environment.yml index 61bd69c2c7a..348dcfbee80 100644 --- a/modules/nf-core/bowtie/align/environment.yml +++ b/modules/nf-core/bowtie/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bowtie2/align/environment.yml b/modules/nf-core/bowtie2/align/environment.yml index 9090f218834..9df1ffc566a 100644 --- a/modules/nf-core/bowtie2/align/environment.yml +++ b/modules/nf-core/bowtie2/align/environment.yml @@ -1,7 +1,12 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: + # renovate: datasource=conda depName=bioconda/bowtie2 - bioconda::bowtie2=2.5.2 + # renovate: datasource=conda depName=bioconda/samtools - bioconda::samtools=1.18 + # renovate: datasource=conda depName=conda-forge/pigz - conda-forge::pigz=2.6 From b615ae27abc0afa0864a14b24c320e39f53e849f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 8 Nov 2024 11:33:06 -0600 Subject: [PATCH 35/59] style: Somehow fix the prettier linting error? --- modules/nf-core/gatk4/mutect2/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index fbeeb1eafc2..a9d234af43a 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 From 4c8ff196d94b7b4cf1273afc211b29b0c1a09447 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Fri, 8 Nov 2024 19:37:44 +0000 Subject: [PATCH 36/59] fix whitespace error --- modules/nf-core/gatk4/addorreplacereadgroups/environment.yml | 2 +- modules/nf-core/gatk4/annotateintervals/environment.yml | 2 +- modules/nf-core/gatk4/applybqsr/environment.yml | 2 +- modules/nf-core/gatk4/applyvqsr/environment.yml | 2 +- modules/nf-core/gatk4/asereadcounter/environment.yml | 2 +- modules/nf-core/gatk4/baserecalibrator/environment.yml | 2 +- modules/nf-core/gatk4/bedtointervallist/environment.yml | 2 +- modules/nf-core/gatk4/calculatecontamination/environment.yml | 2 +- modules/nf-core/gatk4/calibratedragstrmodel/environment.yml | 2 +- modules/nf-core/gatk4/cnnscorevariants/environment.yml | 2 +- modules/nf-core/gatk4/collectreadcounts/environment.yml | 2 +- modules/nf-core/gatk4/collectsvevidence/environment.yml | 2 +- modules/nf-core/gatk4/combinegvcfs/environment.yml | 2 +- modules/nf-core/gatk4/composestrtablefile/environment.yml | 2 +- modules/nf-core/gatk4/condensedepthevidence/environment.yml | 2 +- .../nf-core/gatk4/createreadcountpanelofnormals/environment.yml | 2 +- modules/nf-core/gatk4/createsequencedictionary/environment.yml | 2 +- .../nf-core/gatk4/createsomaticpanelofnormals/environment.yml | 2 +- modules/nf-core/gatk4/denoisereadcounts/environment.yml | 2 +- .../nf-core/gatk4/determinegermlinecontigploidy/environment.yml | 2 +- modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml | 2 +- modules/nf-core/gatk4/fastqtosam/environment.yml | 2 +- modules/nf-core/gatk4/filterintervals/environment.yml | 2 +- modules/nf-core/gatk4/filtermutectcalls/environment.yml | 2 +- modules/nf-core/gatk4/filtervarianttranches/environment.yml | 2 +- modules/nf-core/gatk4/gatherbqsrreports/environment.yml | 2 +- modules/nf-core/gatk4/gatherpileupsummaries/environment.yml | 2 +- modules/nf-core/gatk4/genomicsdbimport/environment.yml | 2 +- modules/nf-core/gatk4/genotypegvcfs/environment.yml | 2 +- modules/nf-core/gatk4/germlinecnvcaller/environment.yml | 2 +- modules/nf-core/gatk4/getpileupsummaries/environment.yml | 2 +- modules/nf-core/gatk4/haplotypecaller/environment.yml | 2 +- modules/nf-core/gatk4/indexfeaturefile/environment.yml | 2 +- modules/nf-core/gatk4/intervallisttobed/environment.yml | 2 +- modules/nf-core/gatk4/intervallisttools/environment.yml | 2 +- modules/nf-core/gatk4/learnreadorientationmodel/environment.yml | 2 +- modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml | 2 +- modules/nf-core/gatk4/markduplicates/environment.yml | 2 +- modules/nf-core/gatk4/mergebamalignment/environment.yml | 2 +- modules/nf-core/gatk4/mergemutectstats/environment.yml | 2 +- modules/nf-core/gatk4/mergevcfs/environment.yml | 2 +- .../nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml | 2 +- modules/nf-core/gatk4/preprocessintervals/environment.yml | 2 +- modules/nf-core/gatk4/printreads/environment.yml | 2 +- modules/nf-core/gatk4/printsvevidence/environment.yml | 2 +- modules/nf-core/gatk4/reblockgvcf/environment.yml | 2 +- modules/nf-core/gatk4/revertsam/environment.yml | 2 +- modules/nf-core/gatk4/samtofastq/environment.yml | 2 +- modules/nf-core/gatk4/selectvariants/environment.yml | 2 +- modules/nf-core/gatk4/shiftfasta/environment.yml | 2 +- modules/nf-core/gatk4/sitedepthtobaf/environment.yml | 2 +- modules/nf-core/gatk4/splitcram/environment.yml | 2 +- modules/nf-core/gatk4/splitintervals/environment.yml | 2 +- modules/nf-core/gatk4/splitncigarreads/environment.yml | 2 +- modules/nf-core/gatk4/svannotate/environment.yml | 2 +- modules/nf-core/gatk4/svcluster/environment.yml | 2 +- modules/nf-core/gatk4/variantfiltration/environment.yml | 2 +- modules/nf-core/gatk4/variantrecalibrator/environment.yml | 2 +- modules/nf-core/gatk4/variantstotable/environment.yml | 2 +- 59 files changed, 59 insertions(+), 59 deletions(-) diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/asereadcounter/environment.yml +++ b/modules/nf-core/gatk4/asereadcounter/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/cnnscorevariants/environment.yml b/modules/nf-core/gatk4/cnnscorevariants/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/environment.yml +++ b/modules/nf-core/gatk4/cnnscorevariants/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectsvevidence/environment.yml b/modules/nf-core/gatk4/collectsvevidence/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/collectsvevidence/environment.yml +++ b/modules/nf-core/gatk4/collectsvevidence/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/condensedepthevidence/environment.yml b/modules/nf-core/gatk4/condensedepthevidence/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/environment.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/fastqtosam/environment.yml b/modules/nf-core/gatk4/fastqtosam/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/fastqtosam/environment.yml +++ b/modules/nf-core/gatk4/fastqtosam/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 501478df17b..e3c622194e6 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -6,6 +6,6 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 - bioconda::htslib=1.19.1 - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printsvevidence/environment.yml b/modules/nf-core/gatk4/printsvevidence/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/printsvevidence/environment.yml +++ b/modules/nf-core/gatk4/printsvevidence/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/reblockgvcf/environment.yml b/modules/nf-core/gatk4/reblockgvcf/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/reblockgvcf/environment.yml +++ b/modules/nf-core/gatk4/reblockgvcf/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/selectvariants/environment.yml b/modules/nf-core/gatk4/selectvariants/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/selectvariants/environment.yml +++ b/modules/nf-core/gatk4/selectvariants/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/shiftfasta/environment.yml b/modules/nf-core/gatk4/shiftfasta/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/shiftfasta/environment.yml +++ b/modules/nf-core/gatk4/shiftfasta/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitcram/environment.yml b/modules/nf-core/gatk4/splitcram/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/splitcram/environment.yml +++ b/modules/nf-core/gatk4/splitcram/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/svannotate/environment.yml +++ b/modules/nf-core/gatk4/svannotate/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/svcluster/environment.yml +++ b/modules/nf-core/gatk4/svcluster/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index fbeeb1eafc2..852054ae15c 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantstotable/environment.yml b/modules/nf-core/gatk4/variantstotable/environment.yml index 7a5362b0171..ea39e501c83 100644 --- a/modules/nf-core/gatk4/variantstotable/environment.yml +++ b/modules/nf-core/gatk4/variantstotable/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 +  - bioconda::gatk4=4.6.1.0 From 8122c8fc795951a13f087dd56c41f465305864bb Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Fri, 8 Nov 2024 19:45:48 +0000 Subject: [PATCH 37/59] linting --- modules/nf-core/gatk4/addorreplacereadgroups/environment.yml | 2 +- modules/nf-core/gatk4/annotateintervals/environment.yml | 2 +- modules/nf-core/gatk4/applybqsr/environment.yml | 2 +- modules/nf-core/gatk4/applyvqsr/environment.yml | 2 +- modules/nf-core/gatk4/asereadcounter/environment.yml | 2 +- modules/nf-core/gatk4/baserecalibrator/environment.yml | 2 +- modules/nf-core/gatk4/bedtointervallist/environment.yml | 2 +- modules/nf-core/gatk4/calculatecontamination/environment.yml | 2 +- modules/nf-core/gatk4/calibratedragstrmodel/environment.yml | 2 +- modules/nf-core/gatk4/cnnscorevariants/environment.yml | 2 +- modules/nf-core/gatk4/collectreadcounts/environment.yml | 2 +- modules/nf-core/gatk4/collectsvevidence/environment.yml | 2 +- modules/nf-core/gatk4/combinegvcfs/environment.yml | 2 +- modules/nf-core/gatk4/composestrtablefile/environment.yml | 2 +- modules/nf-core/gatk4/condensedepthevidence/environment.yml | 2 +- .../gatk4/createreadcountpanelofnormals/environment.yml | 2 +- .../nf-core/gatk4/createsequencedictionary/environment.yml | 2 +- .../nf-core/gatk4/createsomaticpanelofnormals/environment.yml | 2 +- modules/nf-core/gatk4/denoisereadcounts/environment.yml | 2 +- .../gatk4/determinegermlinecontigploidy/environment.yml | 2 +- .../nf-core/gatk4/estimatelibrarycomplexity/environment.yml | 2 +- modules/nf-core/gatk4/fastqtosam/environment.yml | 2 +- modules/nf-core/gatk4/filterintervals/environment.yml | 2 +- modules/nf-core/gatk4/filtermutectcalls/environment.yml | 2 +- modules/nf-core/gatk4/filtervarianttranches/environment.yml | 2 +- modules/nf-core/gatk4/gatherbqsrreports/environment.yml | 2 +- modules/nf-core/gatk4/gatherpileupsummaries/environment.yml | 2 +- modules/nf-core/gatk4/genomicsdbimport/environment.yml | 2 +- modules/nf-core/gatk4/genotypegvcfs/environment.yml | 2 +- modules/nf-core/gatk4/germlinecnvcaller/environment.yml | 2 +- modules/nf-core/gatk4/getpileupsummaries/environment.yml | 2 +- modules/nf-core/gatk4/haplotypecaller/environment.yml | 2 +- modules/nf-core/gatk4/indexfeaturefile/environment.yml | 2 +- modules/nf-core/gatk4/intervallisttobed/environment.yml | 2 +- modules/nf-core/gatk4/intervallisttools/environment.yml | 2 +- .../nf-core/gatk4/learnreadorientationmodel/environment.yml | 2 +- .../nf-core/gatk4/leftalignandtrimvariants/environment.yml | 2 +- modules/nf-core/gatk4/markduplicates/environment.yml | 4 +++- modules/nf-core/gatk4/mergebamalignment/environment.yml | 2 +- modules/nf-core/gatk4/mergemutectstats/environment.yml | 2 +- modules/nf-core/gatk4/mergevcfs/environment.yml | 2 +- .../nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml | 2 +- modules/nf-core/gatk4/preprocessintervals/environment.yml | 2 +- modules/nf-core/gatk4/printreads/environment.yml | 2 +- modules/nf-core/gatk4/printsvevidence/environment.yml | 2 +- modules/nf-core/gatk4/reblockgvcf/environment.yml | 2 +- modules/nf-core/gatk4/revertsam/environment.yml | 2 +- modules/nf-core/gatk4/samtofastq/environment.yml | 2 +- modules/nf-core/gatk4/selectvariants/environment.yml | 2 +- modules/nf-core/gatk4/shiftfasta/environment.yml | 2 +- modules/nf-core/gatk4/sitedepthtobaf/environment.yml | 2 +- modules/nf-core/gatk4/splitcram/environment.yml | 2 +- modules/nf-core/gatk4/splitintervals/environment.yml | 2 +- modules/nf-core/gatk4/splitncigarreads/environment.yml | 2 +- modules/nf-core/gatk4/svannotate/environment.yml | 2 +- modules/nf-core/gatk4/svcluster/environment.yml | 2 +- modules/nf-core/gatk4/variantfiltration/environment.yml | 2 +- modules/nf-core/gatk4/variantrecalibrator/environment.yml | 2 +- modules/nf-core/gatk4/variantstotable/environment.yml | 2 +- 59 files changed, 61 insertions(+), 59 deletions(-) diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/asereadcounter/environment.yml +++ b/modules/nf-core/gatk4/asereadcounter/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/cnnscorevariants/environment.yml b/modules/nf-core/gatk4/cnnscorevariants/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/environment.yml +++ b/modules/nf-core/gatk4/cnnscorevariants/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectsvevidence/environment.yml b/modules/nf-core/gatk4/collectsvevidence/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/collectsvevidence/environment.yml +++ b/modules/nf-core/gatk4/collectsvevidence/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/condensedepthevidence/environment.yml b/modules/nf-core/gatk4/condensedepthevidence/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/environment.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/fastqtosam/environment.yml b/modules/nf-core/gatk4/fastqtosam/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/fastqtosam/environment.yml +++ b/modules/nf-core/gatk4/fastqtosam/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index e3c622194e6..d06a87e04f9 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -6,6 +6,8 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/htslib - bioconda::htslib=1.19.1 + # renovate: datasource=conda depName=bioconda/samtools - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printsvevidence/environment.yml b/modules/nf-core/gatk4/printsvevidence/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/printsvevidence/environment.yml +++ b/modules/nf-core/gatk4/printsvevidence/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/reblockgvcf/environment.yml b/modules/nf-core/gatk4/reblockgvcf/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/reblockgvcf/environment.yml +++ b/modules/nf-core/gatk4/reblockgvcf/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/selectvariants/environment.yml b/modules/nf-core/gatk4/selectvariants/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/selectvariants/environment.yml +++ b/modules/nf-core/gatk4/selectvariants/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/shiftfasta/environment.yml b/modules/nf-core/gatk4/shiftfasta/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/shiftfasta/environment.yml +++ b/modules/nf-core/gatk4/shiftfasta/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitcram/environment.yml b/modules/nf-core/gatk4/splitcram/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/splitcram/environment.yml +++ b/modules/nf-core/gatk4/splitcram/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/svannotate/environment.yml +++ b/modules/nf-core/gatk4/svannotate/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/svcluster/environment.yml +++ b/modules/nf-core/gatk4/svcluster/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index 852054ae15c..a9d234af43a 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantstotable/environment.yml b/modules/nf-core/gatk4/variantstotable/environment.yml index ea39e501c83..fc9c63b0904 100644 --- a/modules/nf-core/gatk4/variantstotable/environment.yml +++ b/modules/nf-core/gatk4/variantstotable/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 -  - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.6.1.0 From bdc0dce5688b3247824847b070c4f867aac60bc0 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Fri, 8 Nov 2024 20:56:22 +0100 Subject: [PATCH 38/59] Update modules/nf-core/gatk4/cnnscorevariants/environment.yml --- modules/nf-core/gatk4/cnnscorevariants/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/gatk4/cnnscorevariants/environment.yml b/modules/nf-core/gatk4/cnnscorevariants/environment.yml index a9d234af43a..da693d88d57 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/environment.yml +++ b/modules/nf-core/gatk4/cnnscorevariants/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - - bioconda::gatk4=4.6.1.0 + - bioconda::gatk4=4.5.0.0 From f135086ad497434e56a23e008e83ab0fc7b0f994 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Tue, 12 Nov 2024 08:05:25 +0000 Subject: [PATCH 39/59] Revert "chore: Add renovate comments to bowtie2 for sanity check" This reverts commit dafbfe9479ee595f3803ca115a7c4a398262c189. --- modules/nf-core/bowtie/align/environment.yml | 2 -- modules/nf-core/bowtie2/align/environment.yml | 5 ----- 2 files changed, 7 deletions(-) diff --git a/modules/nf-core/bowtie/align/environment.yml b/modules/nf-core/bowtie/align/environment.yml index 348dcfbee80..61bd69c2c7a 100644 --- a/modules/nf-core/bowtie/align/environment.yml +++ b/modules/nf-core/bowtie/align/environment.yml @@ -1,5 +1,3 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bowtie2/align/environment.yml b/modules/nf-core/bowtie2/align/environment.yml index 9df1ffc566a..9090f218834 100644 --- a/modules/nf-core/bowtie2/align/environment.yml +++ b/modules/nf-core/bowtie2/align/environment.yml @@ -1,12 +1,7 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - # renovate: datasource=conda depName=bioconda/bowtie2 - bioconda::bowtie2=2.5.2 - # renovate: datasource=conda depName=bioconda/samtools - bioconda::samtools=1.18 - # renovate: datasource=conda depName=conda-forge/pigz - conda-forge::pigz=2.6 From bfd182ebd4112b3d7452b012911aa481f2330e22 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Wed, 13 Nov 2024 13:18:07 +0000 Subject: [PATCH 40/59] try to fix tests --- .../germlinecnvcaller/tests/main.nf.test | 14 +- .../germlinecnvcaller/tests/main.nf.test.snap | 84 ++--------- .../tests/main.nf.test | 14 +- .../tests/main.nf.test.snap | 132 +++--------------- 4 files changed, 54 insertions(+), 190 deletions(-) diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index e7d2e817609..3a86029595e 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -83,7 +83,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + path(process.out.cohortcalls[0][1]).list().sort(), + path(process.out.cohortmodel[0][1]).list().sort(), + path(process.out.casecalls[0][1]).list().sort(), + ).match() } ) } @@ -109,7 +114,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + path(process.out.cohortcalls[0][1]).list().sort(), + path(process.out.cohortmodel[0][1]).list().sort(), + path(process.out.casecalls[0][1]).list().sort(), + ).match() } ) } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap index 7a330e81489..e80ac511c76 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -150,79 +150,23 @@ }, "homo sapiens - bam - stub": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "1": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "2": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "3": [ - "versions.yml:md5,73418764ce886774da2a240630f45aff" - ], - "casecalls": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "cohortcalls": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "cohortmodel": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "versions": [ - "versions.yml:md5,73418764ce886774da2a240630f45aff" - ] - } + [ + "versions.yml:md5,73418764ce886774da2a240630f45aff" + ], + [ + + ], + [ + + ], + [ + + ] ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T20:37:29.536430707" + "timestamp": "2024-11-13T11:41:00.084014901" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test index 2f2b3a0ce25..e0d13a6403a 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -111,7 +111,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.intervals[0][1]).name, + file(process.out.segments[0][1]).name, + file(process.out.denoised[0][1]).name, + ).match() } ) } @@ -135,7 +140,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.intervals[0][1]).name, + file(process.out.segments[0][1]).name, + file(process.out.denoised[0][1]).name, + ).match() } ) } diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap index 7858d1e4bf3..e79b68ae941 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap @@ -1,132 +1,32 @@ { "homo sapiens - counts - stub": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_genotyped_intervals.vcf.gz" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_genotyped_segments.vcf.gz" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_denoised.vcf.gz" - ] - ], - "3": [ - "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" - ], - "denoised": [ - [ - { - "id": "test" - }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_denoised.vcf.gz" - ] - ], - "intervals": [ - [ - { - "id": "test" - }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_genotyped_intervals.vcf.gz" - ] - ], - "segments": [ - [ - { - "id": "test" - }, - "/workspace/nf-core-modules/.nf-test/tests/4b1cf291b9c8de6f7d658b8a467254a1/work/c3/8105a35c1061e39b48bcf378f4be28/test_genotyped_segments.vcf.gz" - ] - ], - "versions": [ - "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" - ] - } + [ + "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" + ], + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz" ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-08T09:09:36.05466689" + "timestamp": "2024-11-13T13:16:30.579209181" }, "homo sapiens - counts": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test_genotyped_intervals.vcf.gz:md5,16185817eecc1818566925612a17e22b" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test_genotyped_segments.vcf.gz:md5,367d6c25a4e825df8e266a62933abf2d" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "/workspace/nf-core-modules/.nf-test/tests/ed5726b677bb1f1830d5f6b92b099cb9/work/57/cfa7ba4c9e3d0425a8cdc02e703820/test_denoised.vcf.gz" - ] - ], - "3": [ - "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" - ], - "denoised": [ - [ - { - "id": "test" - }, - "/workspace/nf-core-modules/.nf-test/tests/ed5726b677bb1f1830d5f6b92b099cb9/work/57/cfa7ba4c9e3d0425a8cdc02e703820/test_denoised.vcf.gz" - ] - ], - "intervals": [ - [ - { - "id": "test" - }, - "test_genotyped_intervals.vcf.gz:md5,16185817eecc1818566925612a17e22b" - ] - ], - "segments": [ - [ - { - "id": "test" - }, - "test_genotyped_segments.vcf.gz:md5,367d6c25a4e825df8e266a62933abf2d" - ] - ], - "versions": [ - "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" - ] - } + [ + "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" + ], + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz" ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-08T09:08:53.062177092" + "timestamp": "2024-11-13T13:15:53.006230234" } } \ No newline at end of file From 2e1bcf3e0bb3f58be36f1276e068495145e2a473 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Wed, 13 Nov 2024 13:45:40 +0000 Subject: [PATCH 41/59] add gcnvkernel to conda env --- modules/nf-core/gatk4/addorreplacereadgroups/environment.yml | 2 ++ modules/nf-core/gatk4/annotateintervals/environment.yml | 2 ++ modules/nf-core/gatk4/applybqsr/environment.yml | 2 ++ modules/nf-core/gatk4/applyvqsr/environment.yml | 2 ++ modules/nf-core/gatk4/asereadcounter/environment.yml | 2 ++ modules/nf-core/gatk4/baserecalibrator/environment.yml | 2 ++ modules/nf-core/gatk4/bedtointervallist/environment.yml | 2 ++ modules/nf-core/gatk4/calculatecontamination/environment.yml | 2 ++ modules/nf-core/gatk4/calibratedragstrmodel/environment.yml | 2 ++ modules/nf-core/gatk4/collectreadcounts/environment.yml | 2 ++ modules/nf-core/gatk4/collectsvevidence/environment.yml | 2 ++ modules/nf-core/gatk4/combinegvcfs/environment.yml | 2 ++ modules/nf-core/gatk4/composestrtablefile/environment.yml | 2 ++ modules/nf-core/gatk4/condensedepthevidence/environment.yml | 2 ++ .../nf-core/gatk4/createreadcountpanelofnormals/environment.yml | 2 ++ modules/nf-core/gatk4/createsequencedictionary/environment.yml | 2 ++ .../nf-core/gatk4/createsomaticpanelofnormals/environment.yml | 2 ++ modules/nf-core/gatk4/denoisereadcounts/environment.yml | 2 ++ .../nf-core/gatk4/determinegermlinecontigploidy/environment.yml | 2 ++ modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml | 2 ++ modules/nf-core/gatk4/fastqtosam/environment.yml | 2 ++ modules/nf-core/gatk4/filterintervals/environment.yml | 2 ++ modules/nf-core/gatk4/filtermutectcalls/environment.yml | 2 ++ modules/nf-core/gatk4/filtervarianttranches/environment.yml | 2 ++ modules/nf-core/gatk4/gatherbqsrreports/environment.yml | 2 ++ modules/nf-core/gatk4/gatherpileupsummaries/environment.yml | 2 ++ modules/nf-core/gatk4/genomicsdbimport/environment.yml | 2 ++ modules/nf-core/gatk4/genotypegvcfs/environment.yml | 2 ++ modules/nf-core/gatk4/germlinecnvcaller/environment.yml | 2 ++ modules/nf-core/gatk4/getpileupsummaries/environment.yml | 2 ++ modules/nf-core/gatk4/haplotypecaller/environment.yml | 2 ++ modules/nf-core/gatk4/indexfeaturefile/environment.yml | 2 ++ modules/nf-core/gatk4/intervallisttobed/environment.yml | 2 ++ modules/nf-core/gatk4/intervallisttools/environment.yml | 2 ++ modules/nf-core/gatk4/learnreadorientationmodel/environment.yml | 2 ++ modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml | 2 ++ modules/nf-core/gatk4/markduplicates/environment.yml | 2 ++ modules/nf-core/gatk4/mergebamalignment/environment.yml | 2 ++ modules/nf-core/gatk4/mergemutectstats/environment.yml | 2 ++ modules/nf-core/gatk4/mergevcfs/environment.yml | 2 ++ modules/nf-core/gatk4/mutect2/environment.yml | 2 ++ .../nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml | 2 ++ modules/nf-core/gatk4/preprocessintervals/environment.yml | 2 ++ modules/nf-core/gatk4/printreads/environment.yml | 2 ++ modules/nf-core/gatk4/printsvevidence/environment.yml | 2 ++ modules/nf-core/gatk4/reblockgvcf/environment.yml | 2 ++ modules/nf-core/gatk4/revertsam/environment.yml | 2 ++ modules/nf-core/gatk4/samtofastq/environment.yml | 2 ++ modules/nf-core/gatk4/selectvariants/environment.yml | 2 ++ modules/nf-core/gatk4/shiftfasta/environment.yml | 2 ++ modules/nf-core/gatk4/sitedepthtobaf/environment.yml | 2 ++ modules/nf-core/gatk4/splitcram/environment.yml | 2 ++ modules/nf-core/gatk4/splitintervals/environment.yml | 2 ++ modules/nf-core/gatk4/splitncigarreads/environment.yml | 2 ++ modules/nf-core/gatk4/svannotate/environment.yml | 2 ++ modules/nf-core/gatk4/svcluster/environment.yml | 2 ++ modules/nf-core/gatk4/variantfiltration/environment.yml | 2 ++ modules/nf-core/gatk4/variantrecalibrator/environment.yml | 2 ++ modules/nf-core/gatk4/variantstotable/environment.yml | 2 ++ 59 files changed, 118 insertions(+) diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/asereadcounter/environment.yml +++ b/modules/nf-core/gatk4/asereadcounter/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/collectsvevidence/environment.yml b/modules/nf-core/gatk4/collectsvevidence/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/collectsvevidence/environment.yml +++ b/modules/nf-core/gatk4/collectsvevidence/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/condensedepthevidence/environment.yml b/modules/nf-core/gatk4/condensedepthevidence/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/environment.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/fastqtosam/environment.yml b/modules/nf-core/gatk4/fastqtosam/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/fastqtosam/environment.yml +++ b/modules/nf-core/gatk4/fastqtosam/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index d06a87e04f9..ec65c32da48 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -7,6 +7,8 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 # renovate: datasource=conda depName=bioconda/htslib - bioconda::htslib=1.19.1 # renovate: datasource=conda depName=bioconda/samtools diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/printsvevidence/environment.yml b/modules/nf-core/gatk4/printsvevidence/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/printsvevidence/environment.yml +++ b/modules/nf-core/gatk4/printsvevidence/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/reblockgvcf/environment.yml b/modules/nf-core/gatk4/reblockgvcf/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/reblockgvcf/environment.yml +++ b/modules/nf-core/gatk4/reblockgvcf/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/selectvariants/environment.yml b/modules/nf-core/gatk4/selectvariants/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/selectvariants/environment.yml +++ b/modules/nf-core/gatk4/selectvariants/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/shiftfasta/environment.yml b/modules/nf-core/gatk4/shiftfasta/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/shiftfasta/environment.yml +++ b/modules/nf-core/gatk4/shiftfasta/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitcram/environment.yml b/modules/nf-core/gatk4/splitcram/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/splitcram/environment.yml +++ b/modules/nf-core/gatk4/splitcram/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/svannotate/environment.yml +++ b/modules/nf-core/gatk4/svannotate/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/svcluster/environment.yml +++ b/modules/nf-core/gatk4/svcluster/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index a9d234af43a..1f7d0824620 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -6,3 +6,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantstotable/environment.yml b/modules/nf-core/gatk4/variantstotable/environment.yml index fc9c63b0904..d04a469c944 100644 --- a/modules/nf-core/gatk4/variantstotable/environment.yml +++ b/modules/nf-core/gatk4/variantstotable/environment.yml @@ -7,3 +7,5 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 From 003869d3396b8665ee54a116bb243d6da7e7b93f Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 14 Nov 2024 09:13:37 +0100 Subject: [PATCH 42/59] Move to wave containers --- modules/nf-core/gatk4/addorreplacereadgroups/main.nf | 4 ++-- modules/nf-core/gatk4/annotateintervals/main.nf | 4 ++-- modules/nf-core/gatk4/applybqsr/main.nf | 4 ++-- modules/nf-core/gatk4/applyvqsr/main.nf | 4 ++-- modules/nf-core/gatk4/asereadcounter/main.nf | 4 ++-- modules/nf-core/gatk4/baserecalibrator/main.nf | 4 ++-- modules/nf-core/gatk4/bedtointervallist/main.nf | 4 ++-- modules/nf-core/gatk4/calculatecontamination/main.nf | 4 ++-- modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 4 ++-- modules/nf-core/gatk4/collectreadcounts/main.nf | 4 ++-- modules/nf-core/gatk4/collectsvevidence/main.nf | 4 ++-- modules/nf-core/gatk4/combinegvcfs/main.nf | 4 ++-- modules/nf-core/gatk4/composestrtablefile/main.nf | 4 ++-- modules/nf-core/gatk4/condensedepthevidence/main.nf | 4 ++-- modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf | 4 ++-- modules/nf-core/gatk4/createsequencedictionary/main.nf | 4 ++-- modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 4 ++-- modules/nf-core/gatk4/denoisereadcounts/main.nf | 4 ++-- modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf | 6 ++++-- modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 4 ++-- modules/nf-core/gatk4/fastqtosam/main.nf | 4 ++-- modules/nf-core/gatk4/filterintervals/main.nf | 4 ++-- modules/nf-core/gatk4/filtermutectcalls/main.nf | 4 ++-- modules/nf-core/gatk4/filtervarianttranches/main.nf | 4 ++-- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 4 ++-- modules/nf-core/gatk4/gatherpileupsummaries/main.nf | 4 ++-- modules/nf-core/gatk4/genomicsdbimport/main.nf | 4 ++-- modules/nf-core/gatk4/genotypegvcfs/main.nf | 4 ++-- modules/nf-core/gatk4/germlinecnvcaller/main.nf | 6 ++++-- modules/nf-core/gatk4/getpileupsummaries/main.nf | 4 ++-- modules/nf-core/gatk4/haplotypecaller/main.nf | 4 ++-- modules/nf-core/gatk4/indexfeaturefile/main.nf | 4 ++-- modules/nf-core/gatk4/intervallisttobed/main.nf | 4 ++-- modules/nf-core/gatk4/intervallisttools/main.nf | 4 ++-- modules/nf-core/gatk4/learnreadorientationmodel/main.nf | 4 ++-- modules/nf-core/gatk4/leftalignandtrimvariants/main.nf | 4 ++-- modules/nf-core/gatk4/mergebamalignment/main.nf | 4 ++-- modules/nf-core/gatk4/mergemutectstats/main.nf | 4 ++-- modules/nf-core/gatk4/mergevcfs/main.nf | 4 ++-- modules/nf-core/gatk4/mutect2/main.nf | 4 ++-- modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf | 6 ++++-- modules/nf-core/gatk4/preprocessintervals/main.nf | 4 ++-- modules/nf-core/gatk4/printreads/main.nf | 4 ++-- modules/nf-core/gatk4/printsvevidence/main.nf | 4 ++-- modules/nf-core/gatk4/reblockgvcf/main.nf | 4 ++-- modules/nf-core/gatk4/revertsam/main.nf | 4 ++-- modules/nf-core/gatk4/samtofastq/main.nf | 4 ++-- modules/nf-core/gatk4/selectvariants/main.nf | 4 ++-- modules/nf-core/gatk4/shiftfasta/main.nf | 4 ++-- modules/nf-core/gatk4/sitedepthtobaf/main.nf | 4 ++-- modules/nf-core/gatk4/splitcram/main.nf | 4 ++-- modules/nf-core/gatk4/splitintervals/main.nf | 4 ++-- modules/nf-core/gatk4/splitncigarreads/main.nf | 4 ++-- modules/nf-core/gatk4/svannotate/main.nf | 4 ++-- modules/nf-core/gatk4/svcluster/main.nf | 4 ++-- modules/nf-core/gatk4/variantfiltration/main.nf | 4 ++-- modules/nf-core/gatk4/variantrecalibrator/main.nf | 4 ++-- modules/nf-core/gatk4/variantstotable/main.nf | 4 ++-- 58 files changed, 122 insertions(+), 116 deletions(-) diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf index 8e0142f943d..12062f75c56 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf +++ b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf @@ -4,8 +4,8 @@ process GATK4_ADDORREPLACEREADGROUPS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/annotateintervals/main.nf b/modules/nf-core/gatk4/annotateintervals/main.nf index e48156d79ec..1f0263758fa 100644 --- a/modules/nf-core/gatk4/annotateintervals/main.nf +++ b/modules/nf-core/gatk4/annotateintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_ANNOTATEINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 7dae410c685..5267454e8ed 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYBQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index e14649aab58..c8ea3da5bf2 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYVQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf b/modules/nf-core/gatk4/asereadcounter/main.nf index 93a3447538d..3f09bffe34d 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf +++ b/modules/nf-core/gatk4/asereadcounter/main.nf @@ -4,8 +4,8 @@ process GATK4_ASEREADCOUNTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam), path(bai), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 3c321159377..4fbf02d606a 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_BASERECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 43db8839ab6..de580fe6da7 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -4,8 +4,8 @@ process GATK4_BEDTOINTERVALLIST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 52f5d194b39..20fe3c5e139 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -4,8 +4,8 @@ process GATK4_CALCULATECONTAMINATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 7e8f50e21df..eb16037b876 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam), path(bam_index) diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 7007d28bfef..7ba74dc65a4 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -4,8 +4,8 @@ process GATK4_COLLECTREADCOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 47c264108c1..b29153dc16f 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_COLLECTSVEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(site_depth_vcf), path(site_depth_vcf_tbi) diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 8b66e3eef7d..1528ac735d5 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_COMBINEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index b6e2ef65a89..71c867cc28c 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -4,8 +4,8 @@ process GATK4_COMPOSESTRTABLEFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: path(fasta) diff --git a/modules/nf-core/gatk4/condensedepthevidence/main.nf b/modules/nf-core/gatk4/condensedepthevidence/main.nf index 0313b46b635..f1f80715426 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/main.nf +++ b/modules/nf-core/gatk4/condensedepthevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_CONDENSEDEPTHEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(depth_evidence), path(depth_evidence_index) diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf index ab22a949721..b754b05cc84 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATEREADCOUNTPANELOFNORMALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(counts) diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index e42735af6b1..fa572145f66 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESEQUENCEDICTIONARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 5213951d6f7..fb6fdf7c04e 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESOMATICPANELOFNORMALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(genomicsdb) diff --git a/modules/nf-core/gatk4/denoisereadcounts/main.nf b/modules/nf-core/gatk4/denoisereadcounts/main.nf index e142262cf1b..6b3d1ea5191 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/main.nf +++ b/modules/nf-core/gatk4/denoisereadcounts/main.nf @@ -4,8 +4,8 @@ process GATK4_DENOISEREADCOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(counts) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index f2eacec8132..af17eac19b6 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -3,8 +3,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.6.1.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(counts), path(bed), path(exclude_beds) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 33eda1ef59f..8fe5cee3039 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -4,8 +4,8 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index acd0e71a527..8d91aa09ab2 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -4,8 +4,8 @@ process GATK4_FASTQTOSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filterintervals/main.nf b/modules/nf-core/gatk4/filterintervals/main.nf index c2a3ccfc4a1..8a6478f6ada 100644 --- a/modules/nf-core/gatk4/filterintervals/main.nf +++ b/modules/nf-core/gatk4/filterintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 927c514ebd6..d3c5bb5ad78 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERMUTECTCALLS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 837b6969287..c5249b7a050 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERVARIANTTRANCHES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 98a71473c2c..275a53c1fce 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -4,8 +4,8 @@ process GATK4_GATHERBQSRREPORTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index 36f1a4123d8..af397a1a2dc 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GATHERPILEUPSUMMARIES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index ce9a7042378..c2b7a07d360 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOMICSDBIMPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index a0fed0699ac..72374179816 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOTYPEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index 2a729f840db..a3ab62426d1 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -2,8 +2,10 @@ process GATK4_GERMLINECNVCALLER { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.6.1.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(tsv), path(intervals), path(ploidy), path(model) diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index af477f818e7..41fd3128118 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GETPILEUPSUMMARIES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 097626064ce..97cd241eea6 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -4,8 +4,8 @@ process GATK4_HAPLOTYPECALLER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index dddb2c111fc..6993537fba0 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -4,8 +4,8 @@ process GATK4_INDEXFEATUREFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index dafcccda5c4..f3cb758006a 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOBED { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 5bf38ab8aad..3ff54bca776 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOOLS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index 2d15b176023..86e7daaa6c6 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_LEARNREADORIENTATIONMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index 0fbccc1a5b3..6087a41872a 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -4,8 +4,8 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index f390eda2317..69027e05305 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEBAMALIGNMENT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index aa74d551fac..e6ddc6994c1 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEMUTECTSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index d9ae935d5f8..683f783bce2 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 044da1822f9..9b45ac22154 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -4,8 +4,8 @@ process GATK4_MUTECT2 { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index fa43dc7b559..835960414ac 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -2,8 +2,10 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.6.1.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(calls), path(model), path(ploidy) diff --git a/modules/nf-core/gatk4/preprocessintervals/main.nf b/modules/nf-core/gatk4/preprocessintervals/main.nf index 0a606275e77..a841a9125a1 100644 --- a/modules/nf-core/gatk4/preprocessintervals/main.nf +++ b/modules/nf-core/gatk4/preprocessintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_PREPROCESSINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf index e24cfa49fb7..3f27661974b 100644 --- a/modules/nf-core/gatk4/printreads/main.nf +++ b/modules/nf-core/gatk4/printreads/main.nf @@ -4,8 +4,8 @@ process GATK4_PRINTREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index d49948ce567..4841391cf7b 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_PRINTSVEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(evidence_files), path(evidence_indices) diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 43376050cb6..4f015396b7a 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -4,8 +4,8 @@ process GATK4_REBLOCKGVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 5ce72543e21..c334d0736d0 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -4,8 +4,8 @@ process GATK4_REVERTSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 2b1484e7da5..37902c78008 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -4,8 +4,8 @@ process GATK4_SAMTOFASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 4e59b3ef9cb..1d18a62b937 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -4,8 +4,8 @@ process GATK4_SELECTVARIANTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(vcf_idx), path (intervals) diff --git a/modules/nf-core/gatk4/shiftfasta/main.nf b/modules/nf-core/gatk4/shiftfasta/main.nf index 8d6874ff6aa..91823f1d6df 100644 --- a/modules/nf-core/gatk4/shiftfasta/main.nf +++ b/modules/nf-core/gatk4/shiftfasta/main.nf @@ -4,8 +4,8 @@ process GATK4_SHIFTFASTA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/sitedepthtobaf/main.nf b/modules/nf-core/gatk4/sitedepthtobaf/main.nf index 185f56f9450..1c6e0ff7a6e 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/main.nf +++ b/modules/nf-core/gatk4/sitedepthtobaf/main.nf @@ -4,8 +4,8 @@ process GATK4_SITEDEPTHTOBAF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(site_depths), path(site_depths_indices) diff --git a/modules/nf-core/gatk4/splitcram/main.nf b/modules/nf-core/gatk4/splitcram/main.nf index 5fd623b7601..66ebd55e4e0 100644 --- a/modules/nf-core/gatk4/splitcram/main.nf +++ b/modules/nf-core/gatk4/splitcram/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITCRAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(cram) diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index db43dfa19c9..01cc5b94af3 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 038613d06b7..9e6fbcb5291 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITNCIGARREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk4/svannotate/main.nf b/modules/nf-core/gatk4/svannotate/main.nf index e76d81c16a7..d81650d6ae6 100644 --- a/modules/nf-core/gatk4/svannotate/main.nf +++ b/modules/nf-core/gatk4/svannotate/main.nf @@ -4,8 +4,8 @@ process GATK4_SVANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(bed) diff --git a/modules/nf-core/gatk4/svcluster/main.nf b/modules/nf-core/gatk4/svcluster/main.nf index 19bd55c63be..5331cd3638d 100644 --- a/modules/nf-core/gatk4/svcluster/main.nf +++ b/modules/nf-core/gatk4/svcluster/main.nf @@ -4,8 +4,8 @@ process GATK4_SVCLUSTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcfs), path(indices) diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index b23f6cf4e9d..5f299fc0b12 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTFILTRATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 317b83ce60a..3c6048f4ba4 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTRECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gatk4/variantstotable/main.nf b/modules/nf-core/gatk4/variantstotable/main.nf index 34ef5a16866..ffa6bc1e7b2 100644 --- a/modules/nf-core/gatk4/variantstotable/main.nf +++ b/modules/nf-core/gatk4/variantstotable/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTSTOTABLE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': - 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(arguments_file), path(include_intervals), path(exclude_intervals) From 1ef16bdfe3f58103b63331733654f399cb4acb8e Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 14 Nov 2024 09:41:37 +0100 Subject: [PATCH 43/59] Update modules/nf-core/gatk4/printsvevidence/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> --- modules/nf-core/gatk4/printsvevidence/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test index 341989aca52..346ca0bddeb 100644 --- a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test @@ -84,7 +84,7 @@ nextflow_process { input_svevidence = files .combine(indices, by:0) .map({ meta, file, index -> - [[], file, index ] + [[id:'test'], file, index ] }) .groupTuple() From 3f82ca1ee929b0905b661d9f34cce769abf02d55 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 14 Nov 2024 09:41:50 +0100 Subject: [PATCH 44/59] Update modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> --- modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test index 9795fbccf94..19a2526f8c2 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test +++ b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test @@ -34,7 +34,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.versions, - file(process.out.vcf[0][1]).name, + path(process.out.vcf[0][1]).vcf.variantsMD5, file(process.out.tbi[0][1]).name, ).match() } ) From 80aba26299ad76b2e265fc018abda4a96566e4d0 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 14 Nov 2024 09:42:04 +0100 Subject: [PATCH 45/59] Update modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> --- .../gatk4/createreadcountpanelofnormals/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test index 55b725861eb..fc14df32574 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test @@ -84,7 +84,7 @@ nextflow_process { process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [[:], tsv ] }) + .map({ meta, tsv -> [[id:'test'], tsv ] }) .groupTuple() """ } From d43bbce370cd8423772e8f0820723b75afdc760c Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 14 Nov 2024 09:42:22 +0100 Subject: [PATCH 46/59] Update modules/nf-core/gatk4/printsvevidence/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> --- modules/nf-core/gatk4/printsvevidence/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test index 346ca0bddeb..6863bc971b4 100644 --- a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test @@ -50,7 +50,7 @@ nextflow_process { input_svevidence = files .combine(indices, by:0) .map({ meta, file, index -> - [[], file, index ] + [[id:'test'], file, index ] }) .groupTuple() From 1d48ca781ca814f06e5ac0907be16f15f56abd24 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 14 Nov 2024 10:00:40 +0100 Subject: [PATCH 47/59] enable conda tests for gatk4 --- .github/workflows/test.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 43fe9733d3a..33cd125c642 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -296,14 +296,6 @@ jobs: tags: fcs/fcsgx - profile: conda tags: gatk4/cnnscorevariants - - profile: conda - tags: gatk4/determinegermlinecontigploidy - - profile: singularity - tags: gatk4/determinegermlinecontigploidy - - profile: conda - tags: gatk4/germlinecnvcaller - - profile: conda - tags: gatk4/postprocessgermlinecnvcalls - profile: conda tags: genescopefk - profile: conda From acb5b568527e3a9eca30adee88285b96a239d889 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 14 Nov 2024 10:38:38 +0000 Subject: [PATCH 48/59] drop params.test_data --- .../gatk4/cnnscorevariants/tests/main.nf.test | 20 ++--- .../tests/main.nf.test | 20 ++--- .../tests/main.nf.test | 14 ++-- .../tests/main.nf.test | 24 +++--- .../filtervarianttranches/tests/main.nf.test | 28 +++---- .../germlinecnvcaller/tests/main.nf.test | 26 +++---- .../intervallisttobed/tests/main.nf.test | 4 +- .../tests/main.nf.test | 26 +++---- .../gatk4/printsvevidence/tests/main.nf.test | 26 +++---- .../gatk4/sitedepthtobaf/tests/main.nf.test | 38 ++++----- .../variantrecalibrator/tests/main.nf.test | 78 +++++++++---------- 11 files changed, 152 insertions(+), 152 deletions(-) diff --git a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test index 19a2526f8c2..ec3ebefce15 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test +++ b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test @@ -15,14 +15,14 @@ nextflow_process { """ input_vcf = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi", checkIfExists: true), [], [] ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) input = [input_vcf, fasta, fai, dict, [], []] """ @@ -51,14 +51,14 @@ nextflow_process { """ input_vcf = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi", checkIfExists: true), [], [] ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) input = [input_vcf, fasta, fai, dict, [], []] """ diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test index fc14df32574..c0ff6adf127 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test @@ -17,9 +17,9 @@ nextflow_process { script "../../preprocessintervals/main.nf" process { """ - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'],checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'],checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'],checkIfExists: true)]).collect() + fasta = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta",checkIfExists: true)]).collect() + fai = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai",checkIfExists: true)]).collect() + dict = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict",checkIfExists: true)]).collect() input[0] = fasta input[1] = fai @@ -36,18 +36,18 @@ nextflow_process { intervals = GATK4_PREPROCESSINTERVALS.out.interval_list.map{ meta, list -> list} input[0] = Channel.of([ [ id:'test', single_end:false ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), ], [ [ id:'test2', single_end:false ], - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), ]) .combine(intervals) - input[1] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'],checkIfExists: true)]).collect() - input[2] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'],checkIfExists: true)]).collect() - input[3] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'],checkIfExists: true)]).collect() + input[1] = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta",checkIfExists: true)]).collect() + input[2] = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai",checkIfExists: true)]).collect() + input[3] = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict",checkIfExists: true)]).collect() """ } } diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test index 1821a00fb66..e9e05764b24 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { script "../../../untar/main.nf" process { """ - input[0] = [[id:'test'], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ] + input[0] = [[id:'test'], file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz", checkIfExists: true) ] """ } } @@ -28,13 +28,13 @@ nextflow_process { """ input[0] = UNTAR.out.untar input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) ] """ } @@ -62,13 +62,13 @@ nextflow_process { """ input[0] = UNTAR.out.untar input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) ] """ } diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test index aa4583c3bc9..b1ad4f517c6 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -16,22 +16,22 @@ nextflow_process { script "../../collectreadcounts/main.nf" process { """ - bed = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) + bed = Channel.of(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) ch_input = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ], [ [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true) ]).combine(bed) - ch_fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - ch_fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - ch_dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() + ch_fasta = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + ch_fai = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + ch_dict = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() input = [ch_input, ch_fasta, ch_fai, ch_dict] """ @@ -44,8 +44,8 @@ nextflow_process { when { process { """ - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) - bed = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) + contig_ploidy_table = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + bed = Channel.of(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) .map({bed -> return bed.text.replaceFirst("0","10001") }) .collectFile( name: "genome_exclude.bed" ) @@ -76,8 +76,8 @@ nextflow_process { when { process { """ - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) - bed = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) + contig_ploidy_table = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + bed = Channel.of(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) .map({bed -> return bed.text.replaceFirst("0","10001") }) .collectFile( name: "genome_exclude.bed" ) diff --git a/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test index f1688c558e2..44c0892a663 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test +++ b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test @@ -17,15 +17,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true), [] ] - input[1] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[4] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[5] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[1] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExists: true) + input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExists: true) + input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[5] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -53,15 +53,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true), [] ] - input[1] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[4] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[5] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[1] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExists: true) + input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExists: true) + input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[5] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index 3a86029595e..e1c7db3d01c 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -21,19 +21,19 @@ nextflow_process { input[0] = Channel.of( [ [ id:'test', single_end:false ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ], [ [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ]) - input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists:true)]) - input[3] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]) + input[1] = Channel.value([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists:true)]) + input[3] = Channel.value([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) """ } @@ -42,8 +42,8 @@ nextflow_process { script "../../determinegermlinecontigploidy/main.nf" process { """ - bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists:true) + bed = Channel.value(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + contig_ploidy_table = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists:true) input[0] = GATK4_COLLECTREADCOUNTS.out.tsv .map({ meta, tsv -> [[id:'test'], tsv ] }) @@ -59,8 +59,8 @@ nextflow_process { script "../../bedtointervallist/main.nf" process { """ - input[0] = Channel.of([[ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)]) - input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]) + input[0] = Channel.of([[ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)]) + input[1] = Channel.value([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) """ } } diff --git a/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test index e801b06654d..57b39481703 100644 --- a/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test +++ b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list", checkIfExists: true) ] """ } @@ -40,7 +40,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list", checkIfExists: true) ] """ } diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test index e0d13a6403a..716323fd4f6 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -19,8 +19,8 @@ nextflow_process { script "../../bedtointervallist/main.nf" process { """ - intervals = [[ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)] - dict = [ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] + intervals = [[ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)] + dict = [ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)] input = [intervals, dict] """ @@ -32,20 +32,20 @@ nextflow_process { """ input_bam = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true), ], [ [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ]) - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() + fasta = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + fai = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + dict = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() input = [input_bam, fasta, fai, dict] """ @@ -55,7 +55,7 @@ nextflow_process { script "../../determinegermlinecontigploidy/main.nf" process { """ - bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) + bed = Channel.value(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) input = [ GATK4_COLLECTREADCOUNTS.out.tsv .map({ meta, tsv -> [[id:'test'], tsv ] }) @@ -63,7 +63,7 @@ nextflow_process { .combine(bed) .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), [[],[]], - file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) ] """ } diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test index 6863bc971b4..23ec217a244 100644 --- a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test @@ -19,22 +19,22 @@ nextflow_process { input[0] = Channel.of( [ [ id:'normal' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), [], [] ], [ [ id:'tumor' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), [], [] ] ) - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[1] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -56,9 +56,9 @@ nextflow_process { input[0] = input_svevidence input[1] = [] - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[4] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -90,9 +90,9 @@ nextflow_process { input[0] = input_svevidence input[1] = [] - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[4] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test index 8d077212605..2d9cf3a4d68 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test @@ -16,28 +16,28 @@ nextflow_process { script "../../collectsvevidence/main.nf" process { """ - vcf = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true) - tbi = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + vcf = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true) + tbi = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) input[0] = Channel.of( [ [ id:'tumor', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), vcf, tbi ], [ [ id:'normal', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), vcf, tbi ] ) - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[1] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -54,12 +54,12 @@ nextflow_process { input[0] = sitedepthtobaf_input input[1] = [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) ] - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[4] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -90,12 +90,12 @@ nextflow_process { input[0] = sitedepthtobaf_input input[1] = [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) ] - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[4] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test index d0878ab7fec..cc19c0a1bc7 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test @@ -15,21 +15,21 @@ nextflow_process { process { """ input_vcf = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) ] resources_vcf = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) ] resources_tbi = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) ] labels = [ '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', @@ -38,9 +38,9 @@ nextflow_process { '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) + fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) + dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] """ @@ -68,21 +68,21 @@ nextflow_process { process { """ input_vcf = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) ] resources_vcf = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) ] resources_tbi = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) ] labels = [ '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', @@ -91,9 +91,9 @@ nextflow_process { '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) + fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) + dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] """ @@ -123,21 +123,21 @@ nextflow_process { process { """ input_vcf = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) ] resources_vcf = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) ] resources_tbi = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), + file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) ] labels = [ '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', @@ -146,9 +146,9 @@ nextflow_process { '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) + fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) + dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] """ From 8d2afd823ebcacc726dde685e011b905777ccd16 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 14 Nov 2024 10:58:01 +0000 Subject: [PATCH 49/59] fix test_data_base --- .../gatk4/cnnscorevariants/tests/main.nf.test | 20 ++--- .../tests/main.nf.test | 20 ++--- .../tests/main.nf.test | 14 ++-- .../tests/main.nf.test | 24 +++--- .../filtervarianttranches/tests/main.nf.test | 28 +++---- .../germlinecnvcaller/tests/main.nf.test | 26 +++---- .../intervallisttobed/tests/main.nf.test | 4 +- .../tests/main.nf.test | 26 +++---- .../gatk4/printsvevidence/tests/main.nf.test | 26 +++---- .../gatk4/sitedepthtobaf/tests/main.nf.test | 38 ++++----- .../variantrecalibrator/tests/main.nf.test | 78 +++++++++---------- 11 files changed, 152 insertions(+), 152 deletions(-) diff --git a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test index ec3ebefce15..db58bf421c1 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test +++ b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test @@ -15,14 +15,14 @@ nextflow_process { """ input_vcf = [ [ id:'test' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi", checkIfExists: true), [], [] ] - fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) input = [input_vcf, fasta, fai, dict, [], []] """ @@ -51,14 +51,14 @@ nextflow_process { """ input_vcf = [ [ id:'test' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi", checkIfExists: true), [], [] ] - fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) input = [input_vcf, fasta, fai, dict, [], []] """ diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test index c0ff6adf127..f16c2df39d8 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test @@ -17,9 +17,9 @@ nextflow_process { script "../../preprocessintervals/main.nf" process { """ - fasta = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta",checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai",checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict",checkIfExists: true)]).collect() + fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta",checkIfExists: true)]).collect() + fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai",checkIfExists: true)]).collect() + dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict",checkIfExists: true)]).collect() input[0] = fasta input[1] = fai @@ -36,18 +36,18 @@ nextflow_process { intervals = GATK4_PREPROCESSINTERVALS.out.interval_list.map{ meta, list -> list} input[0] = Channel.of([ [ id:'test', single_end:false ], - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), ], [ [ id:'test2', single_end:false ], - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), ]) .combine(intervals) - input[1] = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta",checkIfExists: true)]).collect() - input[2] = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai",checkIfExists: true)]).collect() - input[3] = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict",checkIfExists: true)]).collect() + input[1] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta",checkIfExists: true)]).collect() + input[2] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai",checkIfExists: true)]).collect() + input[3] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict",checkIfExists: true)]).collect() """ } } diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test index e9e05764b24..95cb57240bd 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { script "../../../untar/main.nf" process { """ - input[0] = [[id:'test'], file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz", checkIfExists: true) ] + input[0] = [[id:'test'], file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz", checkIfExists: true) ] """ } } @@ -28,13 +28,13 @@ nextflow_process { """ input[0] = UNTAR.out.untar input[1] = [ [ id:'genome' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) ] """ } @@ -62,13 +62,13 @@ nextflow_process { """ input[0] = UNTAR.out.untar input[1] = [ [ id:'genome' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) ] """ } diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test index b1ad4f517c6..088aa7e2fd7 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -16,22 +16,22 @@ nextflow_process { script "../../collectreadcounts/main.nf" process { """ - bed = Channel.of(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) + bed = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) ch_input = Channel.of([ [ id:'test', single_end:false ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ], [ [ id:'test2', single_end:false ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true) ]).combine(bed) - ch_fasta = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() - ch_fai = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() - ch_dict = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() + ch_fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + ch_fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + ch_dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() input = [ch_input, ch_fasta, ch_fai, ch_dict] """ @@ -44,8 +44,8 @@ nextflow_process { when { process { """ - contig_ploidy_table = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) - bed = Channel.of(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) + contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + bed = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) .map({bed -> return bed.text.replaceFirst("0","10001") }) .collectFile( name: "genome_exclude.bed" ) @@ -76,8 +76,8 @@ nextflow_process { when { process { """ - contig_ploidy_table = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) - bed = Channel.of(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) + contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + bed = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) .map({bed -> return bed.text.replaceFirst("0","10001") }) .collectFile( name: "genome_exclude.bed" ) diff --git a/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test index 44c0892a663..c315ed8fc01 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test +++ b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test @@ -17,15 +17,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true), [] ] - input[1] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExists: true) - input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExists: true) - input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - input[5] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -53,15 +53,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true), [] ] - input[1] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExists: true) - input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExists: true) - input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - input[5] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index e1c7db3d01c..4937ce16bba 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -21,19 +21,19 @@ nextflow_process { input[0] = Channel.of( [ [ id:'test', single_end:false ], - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ], [ [ id:'test2', single_end:false ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ]) - input[1] = Channel.value([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists:true)]) - input[3] = Channel.value([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists:true)]) + input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) """ } @@ -42,8 +42,8 @@ nextflow_process { script "../../determinegermlinecontigploidy/main.nf" process { """ - bed = Channel.value(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) - contig_ploidy_table = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists:true) + bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists:true) input[0] = GATK4_COLLECTREADCOUNTS.out.tsv .map({ meta, tsv -> [[id:'test'], tsv ] }) @@ -59,8 +59,8 @@ nextflow_process { script "../../bedtointervallist/main.nf" process { """ - input[0] = Channel.of([[ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)]) - input[1] = Channel.value([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + input[0] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) """ } } diff --git a/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test index 57b39481703..33bf46fbf10 100644 --- a/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test +++ b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list", checkIfExists: true) ] """ } @@ -40,7 +40,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list", checkIfExists: true) ] """ } diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test index 716323fd4f6..6de037b2567 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -19,8 +19,8 @@ nextflow_process { script "../../bedtointervallist/main.nf" process { """ - intervals = [[ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)] - dict = [ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)] + intervals = [[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)] + dict = [ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)] input = [intervals, dict] """ @@ -32,20 +32,20 @@ nextflow_process { """ input_bam = Channel.of([ [ id:'test', single_end:false ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true), ], [ [ id:'test2', single_end:false ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ]) - fasta = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() + fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() input = [input_bam, fasta, fai, dict] """ @@ -55,7 +55,7 @@ nextflow_process { script "../../determinegermlinecontigploidy/main.nf" process { """ - bed = Channel.value(file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) input = [ GATK4_COLLECTREADCOUNTS.out.tsv .map({ meta, tsv -> [[id:'test'], tsv ] }) @@ -63,7 +63,7 @@ nextflow_process { .combine(bed) .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), [[],[]], - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) ] """ } diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test index 23ec217a244..872352ed9a6 100644 --- a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test @@ -19,22 +19,22 @@ nextflow_process { input[0] = Channel.of( [ [ id:'normal' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), [], [] ], [ [ id:'tumor' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), [], [] ] ) - input[1] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -56,9 +56,9 @@ nextflow_process { input[0] = input_svevidence input[1] = [] - input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -90,9 +90,9 @@ nextflow_process { input[0] = input_svevidence input[1] = [] - input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test index 2d9cf3a4d68..1df5fcc81e5 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test @@ -16,28 +16,28 @@ nextflow_process { script "../../collectsvevidence/main.nf" process { """ - vcf = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true) - tbi = file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) + vcf = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true) + tbi = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) input[0] = Channel.of( [ [ id:'tumor', single_end:false ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), vcf, tbi ], [ [ id:'normal', single_end:false ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), vcf, tbi ] ) - input[1] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -54,12 +54,12 @@ nextflow_process { input[0] = sitedepthtobaf_input input[1] = [ - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) ] - input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } @@ -90,12 +90,12 @@ nextflow_process { input[0] = sitedepthtobaf_input input[1] = [ - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) ] - input[2] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) - input[3] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) - input[4] = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test index cc19c0a1bc7..2ce4b46e533 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test @@ -15,21 +15,21 @@ nextflow_process { process { """ input_vcf = [ [ id:'test' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) ] resources_vcf = [ - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) ] resources_tbi = [ - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) ] labels = [ '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', @@ -38,9 +38,9 @@ nextflow_process { '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] - fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) - fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) - dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] """ @@ -68,21 +68,21 @@ nextflow_process { process { """ input_vcf = [ [ id:'test' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) ] resources_vcf = [ - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) ] resources_tbi = [ - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) ] labels = [ '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', @@ -91,9 +91,9 @@ nextflow_process { '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] - fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) - fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) - dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] """ @@ -123,21 +123,21 @@ nextflow_process { process { """ input_vcf = [ [ id:'test' ], // meta map - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) ] resources_vcf = [ - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) ] resources_tbi = [ - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), - file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) ] labels = [ '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', @@ -146,9 +146,9 @@ nextflow_process { '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] - fasta = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) - fai = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) - dict = file("${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] """ From c2da5beeabcc5d5d36878ffc1b3a997128c7ee3b Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 14 Nov 2024 10:58:25 +0000 Subject: [PATCH 50/59] fix createreadcountpanelofnormals snap --- .../tests/main.nf.test.snap | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap index dd30f8981af..630cab6ab2c 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap @@ -18,9 +18,9 @@ "0": [ [ { - + "id": "test" }, - "null.hdf5:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.hdf5:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -29,9 +29,9 @@ "pon": [ [ { - + "id": "test" }, - "null.hdf5:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.hdf5:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -40,9 +40,9 @@ } ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-06T09:11:09.743925974" + "timestamp": "2024-11-14T10:57:07.220349234" } } \ No newline at end of file From fd884916149b995001c3602559724f0bdbedbe67 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 14 Nov 2024 11:07:53 +0000 Subject: [PATCH 51/59] fix printsvevidence snap --- .../printsvevidence/tests/main.nf.test.snap | 101 +++++++----------- 1 file changed, 36 insertions(+), 65 deletions(-) diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap index 18c153e8b9d..74449f9ea1a 100644 --- a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap @@ -1,50 +1,21 @@ { - "sarscov2 - bam - stub": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "2": [ - - ], - "printed_evidence": [ - - ], - "printed_evidence_index": [ - - ], - "versions": [ - - ] - } - ], - "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.0" - }, - "timestamp": "2024-11-04T13:26:54.025037485" - }, "homo sapiens - bam": { "content": [ { "0": [ [ - [ - - ], - "[].pe.txt.gz:md5,e466bbd14a1e511f296f8943ec60ca61" + { + "id": "test" + }, + "test.pe.txt.gz:md5,e466bbd14a1e511f296f8943ec60ca61" ] ], "1": [ [ - [ - - ], - "[].pe.txt.gz.tbi:md5,e56c7481a5f4ff1a14079d9d2bb12a2d" + { + "id": "test" + }, + "test.pe.txt.gz.tbi:md5,e56c7481a5f4ff1a14079d9d2bb12a2d" ] ], "2": [ @@ -52,18 +23,18 @@ ], "printed_evidence": [ [ - [ - - ], - "[].pe.txt.gz:md5,e466bbd14a1e511f296f8943ec60ca61" + { + "id": "test" + }, + "test.pe.txt.gz:md5,e466bbd14a1e511f296f8943ec60ca61" ] ], "printed_evidence_index": [ [ - [ - - ], - "[].pe.txt.gz.tbi:md5,e56c7481a5f4ff1a14079d9d2bb12a2d" + { + "id": "test" + }, + "test.pe.txt.gz.tbi:md5,e56c7481a5f4ff1a14079d9d2bb12a2d" ] ], "versions": [ @@ -72,28 +43,28 @@ } ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-04T13:26:38.860459499" + "timestamp": "2024-11-14T11:03:14.643404627" }, "homo sapiens - bam - stub": { "content": [ { "0": [ [ - [ - - ], - "[].pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + { + "id": "test" + }, + "test.pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ [ - [ - - ], - "[].pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "id": "test" + }, + "test.pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -101,18 +72,18 @@ ], "printed_evidence": [ [ - [ - - ], - "[].pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + { + "id": "test" + }, + "test.pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "printed_evidence_index": [ [ - [ - - ], - "[].pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "id": "test" + }, + "test.pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -121,9 +92,9 @@ } ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T13:15:03.047838982" + "timestamp": "2024-11-14T11:04:00.117599683" } } \ No newline at end of file From cbdab71538f135929cb113d09d0b10d718e45f95 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 14 Nov 2024 13:03:38 +0000 Subject: [PATCH 52/59] fix determinegermlinecontigploidy test --- .../tests/main.nf.test | 17 ++-- .../tests/main.nf.test.snap | 84 +++++++++++++++++-- 2 files changed, 83 insertions(+), 18 deletions(-) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test index 088aa7e2fd7..08734f7d52e 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { script "../../collectreadcounts/main.nf" process { """ - bed = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) + bed = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)) ch_input = Channel.of([ [ id:'test', single_end:false ], // meta map @@ -27,7 +27,8 @@ nextflow_process { [ id:'test2', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true) - ]).combine(bed) + ], + ).combine(bed) ch_fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() ch_fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() @@ -45,15 +46,13 @@ nextflow_process { process { """ contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) - bed = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) - .map({bed -> return bed.text.replaceFirst("0","10001") }) - .collectFile( name: "genome_exclude.bed" ) + bed = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)) input[0] = GATK4_COLLECTREADCOUNTS.out.tsv .map({ meta, tsv -> [[id:'test'] , tsv ] }) .groupTuple() .combine(bed) - .map({ meta, counts, bed -> [ meta, counts, [], bed ]}) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) input[1] = [[],[]] input[2] = contig_ploidy_table """ @@ -77,15 +76,13 @@ nextflow_process { process { """ contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) - bed = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.bed", checkIfExists: true)) - .map({bed -> return bed.text.replaceFirst("0","10001") }) - .collectFile( name: "genome_exclude.bed" ) + bed = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)) input[0] = GATK4_COLLECTREADCOUNTS.out.tsv .map({ meta, tsv -> [[id:'test'] , tsv ] }) .groupTuple() .combine(bed) - .map({ meta, counts, bed -> [ meta, counts, [], bed ]}) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) input[1] = [[],[]] input[2] = contig_ploidy_table """ diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap index 3f480c2bf99..f65ff11afb3 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap @@ -3,30 +3,98 @@ "content": [ { "0": [ - + [ + { + "id": "test" + }, + [ + [ + "contig_ploidy.tsv:md5,bb9e1546d22b4e5b4333b2be09a0842f", + "global_read_depth.tsv:md5,fcfb4903b6809d5c3a215702be918219", + "mu_psi_s_log__.tsv:md5,37ac2b1ab936e55bb4693f0c32576653", + "sample_name.txt:md5,640a474d6f73b01524287f50ca538c04", + "std_psi_s_log__.tsv:md5,b39aaac656630da126669ca7db3fbd02" + ], + [ + "contig_ploidy.tsv:md5,9a57c848331637011b34315f55a248a3", + "global_read_depth.tsv:md5,cd16a368d3779413dbbd0b29b89e78aa", + "mu_psi_s_log__.tsv:md5,dc39aa659e3de51e8db211649b4cd09d", + "sample_name.txt:md5,5cf41871eea16c0fbfdcb7f0f664ed95", + "std_psi_s_log__.tsv:md5,75f4cfece7ec37e84537ddcb6cf713ca" + ] + ] + ] ], "1": [ - + [ + { + "id": "test" + }, + [ + "contig_ploidy_prior.tsv:md5,7a2f5444b09a1f635a540bbcd23176cf", + "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", + "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd", + "mu_mean_bias_j_interval__.tsv:md5,27ae705b7a002517873357ba7ecde39f", + "mu_psi_j_log__.tsv:md5,d3c044b8ba5968ffb62c1e6cb8380f87", + "ploidy_config.json:md5,4cdc16109826fa7d3cdfd1dc8758ec27", + "std_mean_bias_j_interval__.tsv:md5,0816459105b443e6f266e725f298f0b9", + "std_psi_j_log__.tsv:md5,0fe20b8fa4f6da58fe8162cb367bc1b5" + ] + ] ], "2": [ - + "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" ], "calls": [ - + [ + { + "id": "test" + }, + [ + [ + "contig_ploidy.tsv:md5,bb9e1546d22b4e5b4333b2be09a0842f", + "global_read_depth.tsv:md5,fcfb4903b6809d5c3a215702be918219", + "mu_psi_s_log__.tsv:md5,37ac2b1ab936e55bb4693f0c32576653", + "sample_name.txt:md5,640a474d6f73b01524287f50ca538c04", + "std_psi_s_log__.tsv:md5,b39aaac656630da126669ca7db3fbd02" + ], + [ + "contig_ploidy.tsv:md5,9a57c848331637011b34315f55a248a3", + "global_read_depth.tsv:md5,cd16a368d3779413dbbd0b29b89e78aa", + "mu_psi_s_log__.tsv:md5,dc39aa659e3de51e8db211649b4cd09d", + "sample_name.txt:md5,5cf41871eea16c0fbfdcb7f0f664ed95", + "std_psi_s_log__.tsv:md5,75f4cfece7ec37e84537ddcb6cf713ca" + ] + ] + ] ], "model": [ - + [ + { + "id": "test" + }, + [ + "contig_ploidy_prior.tsv:md5,7a2f5444b09a1f635a540bbcd23176cf", + "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", + "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd", + "mu_mean_bias_j_interval__.tsv:md5,27ae705b7a002517873357ba7ecde39f", + "mu_psi_j_log__.tsv:md5,d3c044b8ba5968ffb62c1e6cb8380f87", + "ploidy_config.json:md5,4cdc16109826fa7d3cdfd1dc8758ec27", + "std_mean_bias_j_interval__.tsv:md5,0816459105b443e6f266e725f298f0b9", + "std_psi_j_log__.tsv:md5,0fe20b8fa4f6da58fe8162cb367bc1b5" + ] + ] ], "versions": [ - + "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" ] } ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-06T10:22:21.007041155" + "timestamp": "2024-11-14T12:33:43.844420577" }, "homo sapiens - bam - stub": { "content": [ From dd7551a69cdbe04282f32d1b4d7e27398c15e389 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Fri, 15 Nov 2024 10:32:56 +0000 Subject: [PATCH 53/59] fix? --- .../germlinecnvcaller/tests/main.nf.test | 12 +-- .../germlinecnvcaller/tests/main.nf.test.snap | 82 ++++++++++++++++--- 2 files changed, 72 insertions(+), 22 deletions(-) diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index 4937ce16bba..6fadd50a220 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -85,9 +85,8 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.versions, - path(process.out.cohortcalls[0][1]).list().sort(), - path(process.out.cohortmodel[0][1]).list().sort(), - path(process.out.casecalls[0][1]).list().sort(), + file(process.out.cohortcalls[0][1]).list().sort().name, + file(process.out.cohortmodel[0][1]).list().sort().name, ).match() } ) } @@ -114,12 +113,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.versions, - path(process.out.cohortcalls[0][1]).list().sort(), - path(process.out.cohortmodel[0][1]).list().sort(), - path(process.out.casecalls[0][1]).list().sort(), - ).match() } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap index e80ac511c76..920931b7241 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -150,23 +150,79 @@ }, "homo sapiens - bam - stub": { "content": [ - [ - "versions.yml:md5,73418764ce886774da2a240630f45aff" - ], - [ - - ], - [ - - ], - [ - - ] + { + "0": [ + [ + { + "id": "test" + }, + [ + + ] + ] + ], + "1": [ + [ + { + "id": "test" + }, + [ + + ] + ] + ], + "2": [ + [ + { + "id": "test" + }, + [ + + ] + ] + ], + "3": [ + "versions.yml:md5,73418764ce886774da2a240630f45aff" + ], + "casecalls": [ + [ + { + "id": "test" + }, + [ + + ] + ] + ], + "cohortcalls": [ + [ + { + "id": "test" + }, + [ + + ] + ] + ], + "cohortmodel": [ + [ + { + "id": "test" + }, + [ + + ] + ] + ], + "versions": [ + "versions.yml:md5,73418764ce886774da2a240630f45aff" + ] + } ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-13T11:41:00.084014901" + "timestamp": "2024-11-15T09:52:46.498712189" } } \ No newline at end of file From bbec0ed1fb222b90fbe64255db7b02c023637abb Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 18 Nov 2024 09:07:16 +0000 Subject: [PATCH 54/59] thank you Sateesh --- .../germlinecnvcaller/tests/main.nf.test | 10 +- .../germlinecnvcaller/tests/main.nf.test.snap | 249 +++--------------- 2 files changed, 45 insertions(+), 214 deletions(-) diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index 6fadd50a220..d14ef9a0ff3 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -85,8 +85,8 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.versions, - file(process.out.cohortcalls[0][1]).list().sort().name, - file(process.out.cohortmodel[0][1]).list().sort().name, + file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, + file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, ).match() } ) } @@ -113,7 +113,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, + file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, + ).match() } ) } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap index 920931b7241..bbec501bf87 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -1,228 +1,55 @@ { "homo sapiens - bam": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - [ - [ - "baseline_copy_number_t.tsv:md5,a8f848d75d241f7932ffdca261bffe7b", - "log_c_emission_tc.tsv:md5,02c49de9d58dc21fddeb54b4104f4aab", - "log_q_c_tc.tsv:md5,f6b3b721c503f5406e259f199202ba8c", - "mu_denoised_copy_ratio_t.tsv:md5,8a86b2c88558bae86bb7470f5f00e040", - "mu_psi_s_log__.tsv:md5,fe52c89b83d9c322c2758317235a9bb2", - "mu_read_depth_s_log__.tsv:md5,895d0d31e57004e5f54bdf1b1a3878ae", - "mu_z_su.tsv:md5,f012d75023113664cf03f0e28f41dc40", - "sample_name.txt:md5,5cf41871eea16c0fbfdcb7f0f664ed95", - "std_denoised_copy_ratio_t.tsv:md5,c283b818689b7260b437905e168e0ddb", - "std_psi_s_log__.tsv:md5,ce16b09818baa8da9a580cec33f38c26", - "std_read_depth_s_log__.tsv:md5,4a26cc55bf837f70c658f8e1142cf208", - "std_z_su.tsv:md5,7bc68a10eaec52f5a22d1386af90e2b0" - ], - [ - "baseline_copy_number_t.tsv:md5,51670372d61cf525a2303d293129fc2e", - "log_c_emission_tc.tsv:md5,c9153989adfad01a3f962c03c10cf30e", - "log_q_c_tc.tsv:md5,21bd7ce921286bc416968cce51994c0e", - "mu_denoised_copy_ratio_t.tsv:md5,d47e8bd17cf2f5226fccd369fd2e64b0", - "mu_psi_s_log__.tsv:md5,6d1677b6f7ec7b9538208257f717cc6c", - "mu_read_depth_s_log__.tsv:md5,63ca74e20d21f077f84c2171763512c2", - "mu_z_su.tsv:md5,90659ad8832da4573b7bca9b3146dd96", - "sample_name.txt:md5,640a474d6f73b01524287f50ca538c04", - "std_denoised_copy_ratio_t.tsv:md5,5dfd9d3a38168d6af585b101f0e62ac2", - "std_psi_s_log__.tsv:md5,728b9a2b239665fd68a35f79c6148c50", - "std_read_depth_s_log__.tsv:md5,1f4d0a529de41a661dbf54eb7fed1a93", - "std_z_su.tsv:md5,e3c5e3c96e79a80d234e80fc57734206" - ], - "calling_config.json:md5,dc78889e3d0ba1adf02d10db0194128e", - "denoising_config.json:md5,d2171570b7c746be4d2ce35d9b8db18c", - "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", - "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd" - ] - ] - ], - "1": [ - [ - { - "id": "test" - }, - [ - "calling_config.json:md5,dc78889e3d0ba1adf02d10db0194128e", - "denoising_config.json:md5,d2171570b7c746be4d2ce35d9b8db18c", - "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", - "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd", - "log_q_tau_tk.tsv:md5,0b62b298d25aaa6183f2cc9918b94602", - "mu_W_tu.tsv:md5,d8c78c7a8182eb962f85f82b4a7d477e", - "mu_ard_u_interval__.tsv:md5,13e118b1a505a0c4164974c9dca8036f", - "mu_log_mean_bias_t.tsv:md5,353c41a99919004e377a43772cc430af", - "mu_psi_t_log__.tsv:md5,f776663188dc8b581e556f8a614b68b6", - "std_W_tu.tsv:md5,e075020d8faa4d69ea530a8cecbe75c2", - "std_ard_u_interval__.tsv:md5,151917e122b18c49adf3021409f1ccea", - "std_log_mean_bias_t.tsv:md5,d3257bbec6896549428b8b73f6d7b3a0", - "std_psi_t_log__.tsv:md5,0767d18a424d196aa5a596d03507bc0c" - ] - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,73418764ce886774da2a240630f45aff" - ], - "casecalls": [ - - ], - "cohortcalls": [ - [ - { - "id": "test" - }, - [ - [ - "baseline_copy_number_t.tsv:md5,a8f848d75d241f7932ffdca261bffe7b", - "log_c_emission_tc.tsv:md5,02c49de9d58dc21fddeb54b4104f4aab", - "log_q_c_tc.tsv:md5,f6b3b721c503f5406e259f199202ba8c", - "mu_denoised_copy_ratio_t.tsv:md5,8a86b2c88558bae86bb7470f5f00e040", - "mu_psi_s_log__.tsv:md5,fe52c89b83d9c322c2758317235a9bb2", - "mu_read_depth_s_log__.tsv:md5,895d0d31e57004e5f54bdf1b1a3878ae", - "mu_z_su.tsv:md5,f012d75023113664cf03f0e28f41dc40", - "sample_name.txt:md5,5cf41871eea16c0fbfdcb7f0f664ed95", - "std_denoised_copy_ratio_t.tsv:md5,c283b818689b7260b437905e168e0ddb", - "std_psi_s_log__.tsv:md5,ce16b09818baa8da9a580cec33f38c26", - "std_read_depth_s_log__.tsv:md5,4a26cc55bf837f70c658f8e1142cf208", - "std_z_su.tsv:md5,7bc68a10eaec52f5a22d1386af90e2b0" - ], - [ - "baseline_copy_number_t.tsv:md5,51670372d61cf525a2303d293129fc2e", - "log_c_emission_tc.tsv:md5,c9153989adfad01a3f962c03c10cf30e", - "log_q_c_tc.tsv:md5,21bd7ce921286bc416968cce51994c0e", - "mu_denoised_copy_ratio_t.tsv:md5,d47e8bd17cf2f5226fccd369fd2e64b0", - "mu_psi_s_log__.tsv:md5,6d1677b6f7ec7b9538208257f717cc6c", - "mu_read_depth_s_log__.tsv:md5,63ca74e20d21f077f84c2171763512c2", - "mu_z_su.tsv:md5,90659ad8832da4573b7bca9b3146dd96", - "sample_name.txt:md5,640a474d6f73b01524287f50ca538c04", - "std_denoised_copy_ratio_t.tsv:md5,5dfd9d3a38168d6af585b101f0e62ac2", - "std_psi_s_log__.tsv:md5,728b9a2b239665fd68a35f79c6148c50", - "std_read_depth_s_log__.tsv:md5,1f4d0a529de41a661dbf54eb7fed1a93", - "std_z_su.tsv:md5,e3c5e3c96e79a80d234e80fc57734206" - ], - "calling_config.json:md5,dc78889e3d0ba1adf02d10db0194128e", - "denoising_config.json:md5,d2171570b7c746be4d2ce35d9b8db18c", - "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", - "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd" - ] - ] - ], - "cohortmodel": [ - [ - { - "id": "test" - }, - [ - "calling_config.json:md5,dc78889e3d0ba1adf02d10db0194128e", - "denoising_config.json:md5,d2171570b7c746be4d2ce35d9b8db18c", - "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", - "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd", - "log_q_tau_tk.tsv:md5,0b62b298d25aaa6183f2cc9918b94602", - "mu_W_tu.tsv:md5,d8c78c7a8182eb962f85f82b4a7d477e", - "mu_ard_u_interval__.tsv:md5,13e118b1a505a0c4164974c9dca8036f", - "mu_log_mean_bias_t.tsv:md5,353c41a99919004e377a43772cc430af", - "mu_psi_t_log__.tsv:md5,f776663188dc8b581e556f8a614b68b6", - "std_W_tu.tsv:md5,e075020d8faa4d69ea530a8cecbe75c2", - "std_ard_u_interval__.tsv:md5,151917e122b18c49adf3021409f1ccea", - "std_log_mean_bias_t.tsv:md5,d3257bbec6896549428b8b73f6d7b3a0", - "std_psi_t_log__.tsv:md5,0767d18a424d196aa5a596d03507bc0c" - ] - ] - ], - "versions": [ - "versions.yml:md5,73418764ce886774da2a240630f45aff" - ] - } + [ + "versions.yml:md5,73418764ce886774da2a240630f45aff" + ], + [ + "SAMPLE_0", + "SAMPLE_1", + "calling_config.json", + "denoising_config.json", + "gcnvkernel_version.json", + "interval_list.tsv" + ], + [ + "calling_config.json", + "denoising_config.json", + "gcnvkernel_version.json", + "interval_list.tsv", + "log_q_tau_tk.tsv", + "mu_W_tu.tsv", + "mu_ard_u_interval__.tsv", + "mu_log_mean_bias_t.tsv", + "mu_psi_t_log__.tsv", + "std_W_tu.tsv", + "std_ard_u_interval__.tsv", + "std_log_mean_bias_t.tsv", + "std_psi_t_log__.tsv" + ] ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T20:37:04.485536889" + "timestamp": "2024-11-18T08:51:49.791400262" }, "homo sapiens - bam - stub": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "1": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "2": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "3": [ - "versions.yml:md5,73418764ce886774da2a240630f45aff" - ], - "casecalls": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "cohortcalls": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "cohortmodel": [ - [ - { - "id": "test" - }, - [ - - ] - ] - ], - "versions": [ - "versions.yml:md5,73418764ce886774da2a240630f45aff" - ] - } + [ + "versions.yml:md5,73418764ce886774da2a240630f45aff" + ], + [ + + ], + [ + + ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-15T09:52:46.498712189" + "timestamp": "2024-11-18T08:52:19.983061924" } } \ No newline at end of file From 9fa3385c6242464b507173bea4dd575123ab6bff Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 18 Nov 2024 09:42:38 +0000 Subject: [PATCH 55/59] fix cnnscorevariants --- .../nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap index b10467adfc0..63be00cfee3 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap @@ -4,14 +4,14 @@ [ "versions.yml:md5,7e0d98246eb35725469a53e6fb8acfbf" ], - "test.cnn.vcf.gz", + "34e15624519ba7408d53cb8bb365ffc1", "test.cnn.vcf.gz.tbi" ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-06T11:03:31.465934966" + "timestamp": "2024-11-18T09:39:27.896072791" }, "homo sapiens - vcf - stub": { "content": [ From a8fb9789fce4a771faca468f3989fbb657de4b44 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 18 Nov 2024 10:47:39 +0000 Subject: [PATCH 56/59] fix another one --- .../tests/main.nf.test | 6 +- .../tests/main.nf.test.snap | 107 +++--------------- 2 files changed, 23 insertions(+), 90 deletions(-) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test index 08734f7d52e..a6d0fb7b7e7 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -62,7 +62,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.calls[0][1]).list().sort().collect { path -> file(path).name }, + file(process.out.model[0][1]).list().sort().collect { path -> file(path).name }, + ).match() } ) } diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap index f65ff11afb3..83d018e1edb 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap @@ -1,100 +1,29 @@ { "homo sapiens - bam": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - [ - [ - "contig_ploidy.tsv:md5,bb9e1546d22b4e5b4333b2be09a0842f", - "global_read_depth.tsv:md5,fcfb4903b6809d5c3a215702be918219", - "mu_psi_s_log__.tsv:md5,37ac2b1ab936e55bb4693f0c32576653", - "sample_name.txt:md5,640a474d6f73b01524287f50ca538c04", - "std_psi_s_log__.tsv:md5,b39aaac656630da126669ca7db3fbd02" - ], - [ - "contig_ploidy.tsv:md5,9a57c848331637011b34315f55a248a3", - "global_read_depth.tsv:md5,cd16a368d3779413dbbd0b29b89e78aa", - "mu_psi_s_log__.tsv:md5,dc39aa659e3de51e8db211649b4cd09d", - "sample_name.txt:md5,5cf41871eea16c0fbfdcb7f0f664ed95", - "std_psi_s_log__.tsv:md5,75f4cfece7ec37e84537ddcb6cf713ca" - ] - ] - ] - ], - "1": [ - [ - { - "id": "test" - }, - [ - "contig_ploidy_prior.tsv:md5,7a2f5444b09a1f635a540bbcd23176cf", - "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", - "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd", - "mu_mean_bias_j_interval__.tsv:md5,27ae705b7a002517873357ba7ecde39f", - "mu_psi_j_log__.tsv:md5,d3c044b8ba5968ffb62c1e6cb8380f87", - "ploidy_config.json:md5,4cdc16109826fa7d3cdfd1dc8758ec27", - "std_mean_bias_j_interval__.tsv:md5,0816459105b443e6f266e725f298f0b9", - "std_psi_j_log__.tsv:md5,0fe20b8fa4f6da58fe8162cb367bc1b5" - ] - ] - ], - "2": [ - "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" - ], - "calls": [ - [ - { - "id": "test" - }, - [ - [ - "contig_ploidy.tsv:md5,bb9e1546d22b4e5b4333b2be09a0842f", - "global_read_depth.tsv:md5,fcfb4903b6809d5c3a215702be918219", - "mu_psi_s_log__.tsv:md5,37ac2b1ab936e55bb4693f0c32576653", - "sample_name.txt:md5,640a474d6f73b01524287f50ca538c04", - "std_psi_s_log__.tsv:md5,b39aaac656630da126669ca7db3fbd02" - ], - [ - "contig_ploidy.tsv:md5,9a57c848331637011b34315f55a248a3", - "global_read_depth.tsv:md5,cd16a368d3779413dbbd0b29b89e78aa", - "mu_psi_s_log__.tsv:md5,dc39aa659e3de51e8db211649b4cd09d", - "sample_name.txt:md5,5cf41871eea16c0fbfdcb7f0f664ed95", - "std_psi_s_log__.tsv:md5,75f4cfece7ec37e84537ddcb6cf713ca" - ] - ] - ] - ], - "model": [ - [ - { - "id": "test" - }, - [ - "contig_ploidy_prior.tsv:md5,7a2f5444b09a1f635a540bbcd23176cf", - "gcnvkernel_version.json:md5,aa0ad91e0ff23be94e09e909cf2286d8", - "interval_list.tsv:md5,131b5d98142f8ea5798272ddc1c58cdd", - "mu_mean_bias_j_interval__.tsv:md5,27ae705b7a002517873357ba7ecde39f", - "mu_psi_j_log__.tsv:md5,d3c044b8ba5968ffb62c1e6cb8380f87", - "ploidy_config.json:md5,4cdc16109826fa7d3cdfd1dc8758ec27", - "std_mean_bias_j_interval__.tsv:md5,0816459105b443e6f266e725f298f0b9", - "std_psi_j_log__.tsv:md5,0fe20b8fa4f6da58fe8162cb367bc1b5" - ] - ] - ], - "versions": [ - "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" - ] - } + [ + "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" + ], + [ + "SAMPLE_0", + "SAMPLE_1" + ], + [ + "contig_ploidy_prior.tsv", + "gcnvkernel_version.json", + "interval_list.tsv", + "mu_mean_bias_j_interval__.tsv", + "mu_psi_j_log__.tsv", + "ploidy_config.json", + "std_mean_bias_j_interval__.tsv", + "std_psi_j_log__.tsv" + ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.0" }, - "timestamp": "2024-11-14T12:33:43.844420577" + "timestamp": "2024-11-18T10:16:43.182419213" }, "homo sapiens - bam - stub": { "content": [ From acc1026524b47075f6fa5a0f207d89e5afa46d84 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 19 Nov 2024 09:58:16 +0100 Subject: [PATCH 57/59] Delete .github/workflows/test.yml --- .github/workflows/test.yml | 737 ------------------------------------- 1 file changed, 737 deletions(-) delete mode 100644 .github/workflows/test.yml diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml deleted file mode 100644 index a0f446833f4..00000000000 --- a/.github/workflows/test.yml +++ /dev/null @@ -1,737 +0,0 @@ -name: Run tests -on: - push: - branches: - # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging - - "renovate/**" # branches Renovate creates - pull_request: - branches: [master] - merge_group: - types: [checks_requested] - branches: [master] - workflow_dispatch: - inputs: - runners: - description: "Runners to test on" - type: choice - options: - - "ubuntu-latest" - - "self-hosted" - default: "self-hosted" - -# Cancel if a newer run is started -concurrency: - group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} - cancel-in-progress: true - -env: - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - -jobs: - pre-commit: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.11" - - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 - # FIXME Flip this off once we get to less than a couple hundred. Adding - # this so it will only run against changed files. It'll make it much - # easier to fix these as they come up rather than everything at once. - with: - extra_args: "--all-files" - - prettier: - runs-on: ubuntu-latest - steps: - - name: Check out repository - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - - name: Install NodeJS - uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4 - with: - node-version: "20" - - - name: Install Prettier - run: npm install -g prettier@3.2.5 - - - name: Run Prettier --check - run: prettier --check . - - editorconfig: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - - uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4 - with: - node-version: "20" - - - name: Install editorconfig-checker - run: npm install -g editorconfig-checker - - - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) - - pytest-changes: - name: pytest-changes - runs-on: ubuntu-latest - outputs: - tags: ${{ steps.filter.outputs.changes }} - modules: ${{ steps.tags.outputs.modules }} - subworkflows: ${{ steps.tags.outputs.subworkflows }} - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - with: - fetch-depth: 2 # To retrieve the preceding commit. - - - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3 - id: filter - with: - filters: "tests/config/pytest_modules.yml" - token: "" - - - name: Fetch module tags - id: tags - run: | - echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT - echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT - - - name: debug - run: | - echo ${{ steps.tags.outputs.modules }} - echo ${{ steps.tags.outputs.subworkflows }} - - nf-test-changes: - name: nf-test-changes - runs-on: ubuntu-latest - outputs: - # Expose detected tags as 'modules' and 'workflows' output variables - paths: ${{ steps.list.outputs.components }} - modules: ${{ steps.outputs.outputs.modules }} - subworkflows: ${{ steps.outputs.outputs.subworkflows}} - # Prod for version bumping - - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - with: - fetch-depth: 0 - - - name: List nf-test files - id: list - uses: adamrtalbot/detect-nf-test-changes@7c8be3ffd0d6538312b363c8c949dbbf5f26c3dd # v0.0.4 - with: - head: ${{ github.sha }} - base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }} - n_parents: 2 - - - name: Separate modules and subworkflows - id: outputs - run: | - echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/nf-core/"; ""))') >> $GITHUB_OUTPUT - echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/nf-core/"; ""))') >> $GITHUB_OUTPUT - - - name: debug - run: | - echo ${{ steps.filter.outputs.components }} - echo ${{ steps.outputs.outputs.modules }} - echo ${{ steps.outputs.outputs.subworkflows }} - - nf-core-lint-modules: - runs-on: ${{ github.event.inputs.runners || 'ubuntu-latest' }} - name: nf-core-lint-modules - needs: [pytest-changes, nf-test-changes] - if: ${{ (needs.pytest-changes.outputs.modules != '[]') || ( needs.nf-test-changes.outputs.modules != '[]') }} - strategy: - fail-fast: false - matrix: - tags: - [ - "${{ fromJson(needs.pytest-changes.outputs.modules) }}", - "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", - ] - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - - name: Set up Python - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.11" - - - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4 - id: cache-pip - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip - restore-keys: | - ${{ runner.os }}-pip - - - name: Install pip - run: python -m pip install --upgrade pip - - - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 - with: - distribution: "temurin" - java-version: "17" - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 - - - name: Install nf-core tools development version - run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - - name: Lint module ${{ matrix.tags }} - run: nf-core modules lint ${{ matrix.tags }} - - nf-core-lint-subworkflows: - runs-on: ubuntu-latest - name: nf-core-lint-modules - needs: [pytest-changes, nf-test-changes] - if: ${{ (needs.pytest-changes.outputs.subworkflows != '[]') || ( needs.nf-test-changes.outputs.subworkflows != '[]') }} - strategy: - fail-fast: false - matrix: - tags: - [ - "${{ fromJson(needs.pytest-changes.outputs.subworkflows) }}", - "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}", - ] - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - - name: Set up Python - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.11" - - - name: Install pip - run: python -m pip install --upgrade pip - - - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 - with: - distribution: "temurin" - java-version: "17" - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2 - - - name: Install nf-core tools development version - run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - - name: Lint module ${{ matrix.tags }} - run: nf-core subworkflows lint ${{ matrix.tags }} - - pytest: - runs-on: ${{ github.event.inputs.runners || 'ubuntu-latest' }} - name: pytest - needs: [pytest-changes] - if: needs.pytest-changes.outputs.tags != '[]' - strategy: - fail-fast: false - matrix: - tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"] - profile: [conda, docker, singularity] - exclude: - - tags: nf-test - - profile: conda - tags: backsub - - profile: conda - tags: bases2fastq - - profile: singularity - tags: bases2fastq - - profile: conda - tags: basicpy - - profile: conda - tags: bcl2fastq - - profile: conda - tags: bclconvert - - profile: conda - tags: bwa/aln - - profile: conda - tags: bwa/index - - profile: conda - tags: bwa/mem - - profile: conda - tags: bwa/sampe - - profile: conda - tags: bwa/samse - - profile: conda - tags: cellpose - - profile: conda - tags: cellrangerarc/count - - profile: conda - tags: cellrangerarc/mkfastq - - profile: conda - tags: cellrangerarc/mkref - - profile: conda - tags: cellrangeratac/count - - profile: conda - tags: cellrangeratac/mkfastq - - profile: conda - tags: cellrangeratac/mkref - - profile: conda - tags: checkm2/databasedownload - - profile: conda - tags: checkm2/predict - - profile: conda - tags: controlfreec/makegraph2 - - profile: conda - tags: coreograph - - profile: conda - tags: deepcell/mesmer - - profile: conda - tags: deepvariant - - profile: conda - tags: fastani - - profile: conda - tags: fastk/fastk - - profile: conda - tags: fastk/histex - - profile: conda - tags: fastk/merge - - profile: conda - tags: fcs/fcsadaptor - - profile: conda - tags: fcs/fcsgx - - profile: conda - tags: gatk4/cnnscorevariants - - profile: conda - tags: genescopefk - - profile: conda - tags: happy/sompy - - profile: conda - tags: hlala/preparegraph - - profile: conda - tags: ilastik/multicut - - profile: conda - tags: ilastik/pixelclassification - - profile: conda - tags: imputeme/vcftoprs - - profile: conda - tags: islandpath - - profile: conda - tags: manta/convertinversion - - profile: conda - tags: mcstaging/imc2mc - - profile: conda - tags: mcquant - - profile: conda - tags: medaka - - profile: conda - tags: merquryfk/katcomp - - profile: conda - tags: merquryfk/katgc - - profile: conda - tags: merquryfk/merquryfk - - profile: conda - tags: merquryfk/ploidyplot - - profile: conda - tags: minimap2/align - - profile: conda - tags: mitohifi/findmitoreference - - profile: conda - tags: mitohifi/mitohifi - - profile: conda - tags: nanoplot - - profile: conda - tags: ncbitools/vecscreen - - profile: conda - tags: parabricks/dbsnp - - profile: conda - tags: parabricks/deepvariant - - profile: conda - tags: parabricks/genotypegvcf - - profile: conda - tags: parabricks/haplotypecaller - - profile: conda - tags: parabricks/indexgvcf - - profile: conda - tags: parabricks/mutectcaller - - profile: conda - tags: picard/collecthsmetrics - - profile: conda - tags: picard/collectwgsmetrics - - profile: conda - tags: sentieon/applyvarcal - - profile: conda - tags: sentieon/datametrics - - profile: conda - tags: sentieon/dnamodelapply - - profile: conda - tags: sentieon/dnascope - - profile: conda - tags: sentieon/readwriter - - profile: conda - tags: sentieon/tnfilter - - profile: conda - tags: sentieon/tnhaplotyper2 - - profile: conda - tags: sentieon/tnscope - - profile: conda - tags: sentieon/varcal - - profile: conda - tags: sentieon/wgsmetrics - - profile: conda - tags: subworkflows/bam_qc_picard - - profile: conda - tags: subworkflows/bcl_demultiplex - - profile: conda - tags: subworkflows/fasta_clean_fcs - - profile: conda - tags: svanalyzer/svbenchmark - - profile: conda - tags: universc - - profile: singularity - tags: universc - - profile: conda - tags: vt/decompose - env: - NXF_ANSI_LOG: false - - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - - name: Set up Python - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.11" - - - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4 - id: cache-pip-pytest - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-pytest - restore-keys: | - ${{ runner.os }}-pip-pytest - - - name: Install Python dependencies - run: python -m pip install --upgrade pip pytest-workflow cryptography - - - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 - with: - distribution: "temurin" - java-version: "17" - - name: Setup Nextflow ${{ matrix.NXF_VER }} - uses: nf-core/setup-nextflow@v2 - with: - version: "${{ matrix.NXF_VER }}" - - - name: Setup apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up miniconda - uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3 - with: - miniconda-version: "latest" - channels: conda-forge,bioconda - python-version: ${{ matrix.python-version }} - conda-remove-defaults: true - - - name: Conda setup - run: | - conda clean -a - conda install -n base conda-libmamba-solver - conda config --set solver libmamba - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - # Test the module - - name: Run pytest-workflow - # only use one thread for pytest-workflow to avoid race condition on conda cache. - run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes - - - name: Output log on failure - if: failure() - run: | - sudo apt-get update > /dev/null - sudo apt-get install bat > /dev/null - batcat --decorations=always --color=always /home/ubuntu/pytest_workflow_*/*/log.{out,err} - - - name: Setting global variables - uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 - id: parsed - with: - script: | - return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"') - result-encoding: string - - - name: Upload logs on failure - if: failure() - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 - with: - name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} - path: | - /home/ubuntu/pytest_workflow_*/*/.nextflow.log - /home/ubuntu/pytest_workflow_*/*/log.out - /home/ubuntu/pytest_workflow_*/*/log.err - /home/ubuntu/pytest_workflow_*/*/work - !/home/ubuntu/pytest_workflow_*/*/work/conda - !/home/ubuntu/pytest_workflow_*/*/work/singularity - !${{ github.workspace }}/.singularity - - nf-test: - runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: nf-test - needs: [nf-test-changes] - if: ( needs.nf-test-changes.outputs.paths != '[]' ) - strategy: - fail-fast: false - matrix: - path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"] - profile: [conda, docker_self_hosted, singularity] - exclude: - - path: modules/nf-core/nf-test - - profile: conda - path: modules/nf-core/angsd/gl - - profile: conda - path: modules/nf-core/annotsv/installannotations - - profile: conda - path: modules/nf-core/happy/sompy - - profile: conda - path: modules/nf-core/backsub - - profile: conda - path: modules/nf-core/bakta/bakta - - profile: conda - path: modules/nf-core/bakta/baktadbdownload - - profile: conda - path: modules/nf-core/bases2fastq - - profile: conda - path: modules/nf-core/bcl2fastq - - profile: conda - path: modules/nf-core/bclconvert - - profile: conda - path: modules/nf-core/celesta - - profile: conda - path: modules/nf-core/cellpose - - profile: conda - path: modules/nf-core/cellranger/count - - profile: conda - path: modules/nf-core/cellranger/mkfastq - - profile: conda - path: modules/nf-core/cellranger/mkgtf - - profile: conda - path: modules/nf-core/cellranger/mkref - - profile: conda - path: modules/nf-core/cellranger/mkvdjref - - profile: conda - path: modules/nf-core/cellranger/multi - - profile: conda - path: modules/nf-core/cellranger/vdj - - profile: conda - path: modules/nf-core/checkqc - - profile: conda - path: modules/nf-core/custom/dumpsoftwareversions - - profile: conda - path: modules/nf-core/deepcell/mesmer - - profile: conda - path: modules/nf-core/deepsomatic - - profile: singularity - path: modules/nf-core/deepsomatic - - profile: conda - path: modules/nf-core/deepvariant - - profile: conda - path: modules/nf-core/deepvariant/callvariants - - profile: conda - path: modules/nf-core/deepvariant/makeexamples - - profile: conda - path: modules/nf-core/deepvariant/postprocessvariants - - profile: conda - path: modules/nf-core/deepvariant/rundeepvariant - - profile: conda - path: modules/nf-core/deepvariant/vcfstatsreport - - profile: conda - path: modules/nf-core/doubletdetection - - profile: conda - path: modules/nf-core/ensemblvep/vep - - profile: conda - path: modules/nf-core/fastk/fastk - - profile: conda - path: modules/nf-core/cellrangerarc/mkgtf - - profile: conda - path: modules/nf-core/fastk/histex - - profile: conda - path: modules/nf-core/fastk/merge - - profile: conda - path: modules/nf-core/fcs/fcsadaptor - - profile: conda - path: modules/nf-core/fcs/fcsgx - - profile: conda - path: modules/nf-core/ganon/buildcustom - - profile: conda - path: modules/nf-core/ganon/classify - - profile: conda - path: modules/nf-core/ganon/report - - profile: conda - path: modules/nf-core/ganon/table - - profile: conda - path: modules/nf-core/gatk4/cnnscorevariants - - profile: conda - path: modules/nf-core/gatk4/determinegermlinecontigploidy - - profile: conda - path: modules/nf-core/genescopefk - - profile: conda - path: modules/nf-core/ilastik/multicut - - profile: conda - path: modules/nf-core/ilastik/pixelclassification - - profile: conda - path: modules/nf-core/imputeme/vcftoprs - - profile: conda - path: modules/nf-core/mcstaging/imc2mc - - profile: conda - path: modules/nf-core/mcquant - - profile: conda - path: modules/nf-core/mcstaging/phenoimager2mc - - profile: conda - path: modules/nf-core/merquryfk/katcomp - - profile: conda - path: modules/nf-core/merquryfk/katgc - - profile: conda - path: modules/nf-core/merquryfk/merquryfk - - profile: conda - path: modules/nf-core/merquryfk/ploidyplot - - profile: conda - path: modules/nf-core/molkartgarage/clahe - - profile: conda - path: modules/nf-core/quartonotebook - - profile: conda - path: modules/nf-core/scimap/spatiallda - - profile: conda - path: modules/nf-core/sentieon/bwaindex - - profile: conda - path: modules/nf-core/sentieon/bwamem - - profile: conda - path: modules/nf-core/sentieon/datametrics - - profile: conda - path: modules/nf-core/sentieon/dedup - - profile: conda - path: modules/nf-core/sentieon/qualcal - - profile: conda - path: modules/nf-core/spaceranger/mkgtf - - profile: conda - path: modules/nf-core/spaceranger/mkref - - profile: conda - path: modules/nf-core/spaceranger/count - - profile: conda - path: modules/nf-core/spotiflow - - profile: conda - path: modules/nf-core/svanalyzer/svbenchmark - - profile: conda - path: modules/nf-core/universc - - profile: singularity - path: modules/nf-core/universc - - profile: conda - path: modules/nf-core/vt/decompose - - profile: singularity - path: modules/nf-core/bases2fastq - - profile: conda - path: modules/nf-core/wittyer - - profile: conda - path: modules/nf-core/islandpath - - profile: conda - path: modules/nf-core/scimap/mcmicro - - profile: conda - path: subworkflows/nf-core/vcf_annotate_ensemblvep - - profile: conda - path: subworkflows/nf-core/bcl_demultiplex - - profile: conda - path: subworkflows/nf-core/deepvariant - - profile: conda - path: subworkflows/nf-core/fastq_align_bamcmp_bwa - - profile: conda - path: subworkflows/nf-core/fastq_align_bwa - - profile: conda - path: subworkflows/nf-core/fasta_newick_epang_gappa - - path: modules/nf-core/parabricks/fq2bammeth - - path: modules/nf-core/parabricks/fq2bam - - path: modules/nf-core/parabricks/applybqsr - - profile: conda - path: modules/nf-core/xeniumranger/relabel - - profile: conda - path: modules/nf-core/xeniumranger/rename - - profile: conda - path: modules/nf-core/xeniumranger/resegment - - profile: conda - path: modules/nf-core/xeniumranger/import-segmentation - - env: - NXF_ANSI_LOG: false - - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - - name: Run nf-test Action - uses: ./.github/actions/nf-test-action - with: - path: ${{ matrix.path }} - profile: ${{ matrix.profile }} - - nf-test-gpu: - runs-on: "gpu" - name: nf-test-gpu - needs: [nf-test-changes] - if: ( needs.nf-test-changes.outputs.paths != '[]' && contains(needs.nf-test-changes.outputs.paths, 'modules/nf-core/parabricks') ) - strategy: - fail-fast: false - matrix: - include: - - path: modules/nf-core/parabricks/applybqsr - profile: [docker_self_hosted, singularity] - - path: modules/nf-core/parabricks/fq2bam - profile: [docker_self_hosted, singularity] - - path: modules/nf-core/parabricks/fq2bammeth - profile: [docker_self_hosted, singularity] - env: - NXF_ANSI_LOG: false - - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - - name: Run nf-test Action - uses: ./.github/actions/nf-test-action - env: - SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} - SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} - SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} - SENTIEON_AUTH_MECH: "GitHub Actions - token" - with: - path: ${{ matrix.path }} - profile: ${{ matrix.profile }},gpu - - confirm-pass: - runs-on: ubuntu-latest - needs: - [ - prettier, - editorconfig, - pytest-changes, - nf-core-lint-modules, - nf-core-lint-subworkflows, - pytest, - nf-test-changes, - nf-test, - nf-test-gpu, - ] - if: always() - steps: - - name: All tests ok - if: ${{ success() || !contains(needs.*.result, 'failure') }} - run: exit 0 - - name: One or more tests failed - if: ${{ contains(needs.*.result, 'failure') }} - run: exit 1 - - - name: debug-print - if: always() - run: | - echo "toJSON(needs) = ${{ toJSON(needs) }}" - echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" From c747a5fc92424639bd3c7d4c9b1913ea4b944be0 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:47:03 +0100 Subject: [PATCH 58/59] further enable conda --- .../nf-core/gatk4/determinegermlinecontigploidy/main.nf | 8 -------- modules/nf-core/gatk4/germlinecnvcaller/main.nf | 8 -------- modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf | 8 -------- 3 files changed, 24 deletions(-) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index af17eac19b6..6edccf6117e 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -22,10 +22,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def intervals = bed ? "--intervals ${bed}" : "" @@ -65,10 +61,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." - } prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}-calls diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index a3ab62426d1..e8afb1fbf1a 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -20,10 +20,6 @@ process GATK4_GERMLINECNVCALLER { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def intervals_command = intervals ? "--intervals ${intervals}" : "" @@ -61,10 +57,6 @@ process GATK4_GERMLINECNVCALLER { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." - } def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir -p ${prefix}-cnv-calls/${prefix}-calls diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index 835960414ac..8bb7420d3f5 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -20,10 +20,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def calls_command = calls ? calls.collect{"--calls-shard-path $it"}.join(' ') : "" @@ -57,10 +53,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." - } def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_genotyped_intervals.vcf.gz From 1f6656b48a61a6b19ff51dd66f5b56e8b6a89b33 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Tue, 19 Nov 2024 12:21:29 +0000 Subject: [PATCH 59/59] lower resource labels since gatk is single core at best --- modules/nf-core/gatk4/bedtointervallist/main.nf | 2 +- modules/nf-core/gatk4/collectreadcounts/main.nf | 2 +- modules/nf-core/gatk4/createsequencedictionary/main.nf | 2 +- modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 2 +- modules/nf-core/gatk4/fastqtosam/main.nf | 2 +- modules/nf-core/gatk4/filterintervals/main.nf | 2 +- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 2 +- modules/nf-core/gatk4/genomicsdbimport/main.nf | 2 +- modules/nf-core/gatk4/genotypegvcfs/main.nf | 2 +- modules/nf-core/gatk4/haplotypecaller/main.nf | 2 +- modules/nf-core/gatk4/intervallisttools/main.nf | 2 +- modules/nf-core/gatk4/markduplicates/main.nf | 2 +- modules/nf-core/gatk4/mergevcfs/main.nf | 2 +- modules/nf-core/gatk4/mutect2/main.nf | 2 +- modules/nf-core/gatk4/preprocessintervals/main.nf | 2 +- modules/nf-core/gatk4/revertsam/main.nf | 2 +- modules/nf-core/gatk4/samtofastq/main.nf | 2 +- modules/nf-core/gatk4/selectvariants/main.nf | 2 +- modules/nf-core/gatk4/splitncigarreads/main.nf | 2 +- modules/nf-core/gatk4/variantfiltration/main.nf | 2 +- modules/nf-core/gatk4/variantstotable/main.nf | 2 +- 21 files changed, 21 insertions(+), 21 deletions(-) diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index de580fe6da7..89960e04cac 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -1,6 +1,6 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 7ba74dc65a4..c742a16b178 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -1,6 +1,6 @@ process GATK4_COLLECTREADCOUNTS { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index fa572145f66..998622a0658 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -1,6 +1,6 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 8fe5cee3039..9071279577f 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -1,6 +1,6 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 8d91aa09ab2..e79f847aa04 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -1,6 +1,6 @@ process GATK4_FASTQTOSAM { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/filterintervals/main.nf b/modules/nf-core/gatk4/filterintervals/main.nf index 8a6478f6ada..ada752daf1d 100644 --- a/modules/nf-core/gatk4/filterintervals/main.nf +++ b/modules/nf-core/gatk4/filterintervals/main.nf @@ -1,6 +1,6 @@ process GATK4_FILTERINTERVALS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 275a53c1fce..fdc5a2a723d 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -1,6 +1,6 @@ process GATK4_GATHERBQSRREPORTS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index c2b7a07d360..90f1200dc7a 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -1,6 +1,6 @@ process GATK4_GENOMICSDBIMPORT { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 72374179816..dc2813a350c 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -1,6 +1,6 @@ process GATK4_GENOTYPEGVCFS { tag "$meta.id" - label 'process_high' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 97cd241eea6..1ef76789de5 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -1,6 +1,6 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 3ff54bca776..bf20d4c9372 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -1,6 +1,6 @@ process GATK4_INTERVALLISTTOOLS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index baadefef41f..cf770308d59 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -1,6 +1,6 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 683f783bce2..1752f48a604 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -1,6 +1,6 @@ process GATK4_MERGEVCFS { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 9b45ac22154..3ac374e0356 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -1,6 +1,6 @@ process GATK4_MUTECT2 { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/preprocessintervals/main.nf b/modules/nf-core/gatk4/preprocessintervals/main.nf index a841a9125a1..bab63495898 100644 --- a/modules/nf-core/gatk4/preprocessintervals/main.nf +++ b/modules/nf-core/gatk4/preprocessintervals/main.nf @@ -1,6 +1,6 @@ process GATK4_PREPROCESSINTERVALS { tag "$fasta" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index c334d0736d0..ad2d38ab446 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -1,6 +1,6 @@ process GATK4_REVERTSAM { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 37902c78008..7760d4581bf 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -1,6 +1,6 @@ process GATK4_SAMTOFASTQ { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 1d18a62b937..f93888e6381 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -1,6 +1,6 @@ process GATK4_SELECTVARIANTS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 9e6fbcb5291..40bfee1b30a 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -1,6 +1,6 @@ process GATK4_SPLITNCIGARREADS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index 5f299fc0b12..5bf0e3536d3 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -1,6 +1,6 @@ process GATK4_VARIANTFILTRATION { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/variantstotable/main.nf b/modules/nf-core/gatk4/variantstotable/main.nf index ffa6bc1e7b2..3dbb40af739 100644 --- a/modules/nf-core/gatk4/variantstotable/main.nf +++ b/modules/nf-core/gatk4/variantstotable/main.nf @@ -1,6 +1,6 @@ process GATK4_VARIANTSTOTABLE { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?