From d92691f118b2798acfb6432674668462137e8b88 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Sun, 1 Dec 2024 07:29:48 +0000 Subject: [PATCH 1/8] quanmts-utils 0.0.15 -> 0.0.16 --- modules/local/add_sage_feat/main.nf | 6 +++--- modules/local/diannconvert/main.nf | 6 +++--- modules/local/extract_psm/main.nf | 6 +++--- modules/local/extract_sample/main.nf | 6 +++--- modules/local/generate_diann_cfg/main.nf | 6 +++--- modules/local/ms2rescore/main.nf | 6 +++--- modules/local/mzmlstatistics/main.nf | 6 +++--- modules/local/preprocess_expdesign.nf | 6 +++--- modules/local/samplesheet_check.nf | 6 +++--- modules/local/sdrfparsing/main.nf | 6 +++--- modules/local/spectrum2features/main.nf | 6 +++--- 11 files changed, 33 insertions(+), 33 deletions(-) diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf index 6acef0c4..5be1fe39 100644 --- a/modules/local/add_sage_feat/main.nf +++ b/modules/local/add_sage_feat/main.nf @@ -2,10 +2,10 @@ process SAGEFEATURE { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: tuple val(meta), path(id_file), path(extra_feat) diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf index e8bdfd99..9c728564 100644 --- a/modules/local/diannconvert/main.nf +++ b/modules/local/diannconvert/main.nf @@ -2,10 +2,10 @@ process DIANNCONVERT { tag "$meta.experiment_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: path(report) diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf index 58899a54..70612680 100644 --- a/modules/local/extract_psm/main.nf +++ b/modules/local/extract_psm/main.nf @@ -2,10 +2,10 @@ process PSMCONVERSION { tag "$meta.mzml_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf index 3a67e9e1..11c274da 100644 --- a/modules/local/extract_sample/main.nf +++ b/modules/local/extract_sample/main.nf @@ -2,10 +2,10 @@ process GETSAMPLE { tag "$design.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf index 768db3ae..69cd4080 100644 --- a/modules/local/generate_diann_cfg/main.nf +++ b/modules/local/generate_diann_cfg/main.nf @@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG { tag "$meta.experiment_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: val(meta) diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf index e02a743f..fa0f87f4 100644 --- a/modules/local/ms2rescore/main.nf +++ b/modules/local/ms2rescore/main.nf @@ -2,10 +2,10 @@ process MS2RESCORE { tag "$meta.mzml_id" label 'process_high' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" // userEmulation settings when docker is specified containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${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/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf index 29918840..a9c5bd5b 100644 --- a/modules/local/mzmlstatistics/main.nf +++ b/modules/local/mzmlstatistics/main.nf @@ -3,10 +3,10 @@ process MZMLSTATISTICS { label 'process_very_low' label 'process_single' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: tuple val(meta), path(ms_file) diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf index 02937cb8..39b315c3 100644 --- a/modules/local/preprocess_expdesign.nf +++ b/modules/local/preprocess_expdesign.nf @@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN { tag "$design.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: path design diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index f7c46fbc..0ca6187c 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK { tag "$input_file" label 'process_single' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: path input_file diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf index 393c11e0..65cf9b95 100644 --- a/modules/local/sdrfparsing/main.nf +++ b/modules/local/sdrfparsing/main.nf @@ -2,10 +2,10 @@ process SDRFPARSING { tag "$sdrf.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: path sdrf diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf index 27cbb4ee..3035b4a9 100644 --- a/modules/local/spectrum2features/main.nf +++ b/modules/local/spectrum2features/main.nf @@ -2,10 +2,10 @@ process SPECTRUM2FEATURES { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" input: tuple val(meta), path(id_file), path(ms_file) From 369cda15d2a048850b668884d45903401af45be5 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 3 Dec 2024 16:16:44 +0000 Subject: [PATCH 2/8] added quantms-rescoring 0.0.1 --- modules/local/ms2rescore/main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf index fa0f87f4..49bb1cc4 100644 --- a/modules/local/ms2rescore/main.nf +++ b/modules/local/ms2rescore/main.nf @@ -2,10 +2,10 @@ process MS2RESCORE { tag "$meta.mzml_id" label 'process_high' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-rescoring=0.0.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.1--pyhdfd78af_0' : + 'biocontainers/quantms-rescoring:0.0.1--pyhdfd78af_0' }" // userEmulation settings when docker is specified containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : '' @@ -43,7 +43,7 @@ process MS2RESCORE { } """ - quantmsutilsc ms2rescore \\ + rescoring ms2rescore \\ --psm_file $idxml \\ --spectrum_path . \\ --ms2_tolerance $ms2_tolerence \\ From 98d08611b5451f8bb3540e85be4c7896be9f4478 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 3 Dec 2024 16:47:05 +0000 Subject: [PATCH 3/8] replace quantms-utils 0.0.16 -> 0.0.17 --- modules/local/add_sage_feat/main.nf | 6 +++--- modules/local/diannconvert/main.nf | 6 +++--- modules/local/extract_psm/main.nf | 6 +++--- modules/local/extract_sample/main.nf | 6 +++--- modules/local/generate_diann_cfg/main.nf | 6 +++--- modules/local/mzmlstatistics/main.nf | 6 +++--- modules/local/preprocess_expdesign.nf | 6 +++--- modules/local/samplesheet_check.nf | 6 +++--- modules/local/sdrfparsing/main.nf | 6 +++--- modules/local/spectrum2features/main.nf | 6 +++--- 10 files changed, 30 insertions(+), 30 deletions(-) diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf index 5be1fe39..6c014fde 100644 --- a/modules/local/add_sage_feat/main.nf +++ b/modules/local/add_sage_feat/main.nf @@ -2,10 +2,10 @@ process SAGEFEATURE { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: tuple val(meta), path(id_file), path(extra_feat) diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf index 9c728564..d3adbe8b 100644 --- a/modules/local/diannconvert/main.nf +++ b/modules/local/diannconvert/main.nf @@ -2,10 +2,10 @@ process DIANNCONVERT { tag "$meta.experiment_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: path(report) diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf index 70612680..68018636 100644 --- a/modules/local/extract_psm/main.nf +++ b/modules/local/extract_psm/main.nf @@ -2,10 +2,10 @@ process PSMCONVERSION { tag "$meta.mzml_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf index 11c274da..5106f0ab 100644 --- a/modules/local/extract_sample/main.nf +++ b/modules/local/extract_sample/main.nf @@ -2,10 +2,10 @@ process GETSAMPLE { tag "$design.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf index 69cd4080..eb8209f1 100644 --- a/modules/local/generate_diann_cfg/main.nf +++ b/modules/local/generate_diann_cfg/main.nf @@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG { tag "$meta.experiment_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: val(meta) diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf index a9c5bd5b..169d8789 100644 --- a/modules/local/mzmlstatistics/main.nf +++ b/modules/local/mzmlstatistics/main.nf @@ -3,10 +3,10 @@ process MZMLSTATISTICS { label 'process_very_low' label 'process_single' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: tuple val(meta), path(ms_file) diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf index 39b315c3..03b066ba 100644 --- a/modules/local/preprocess_expdesign.nf +++ b/modules/local/preprocess_expdesign.nf @@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN { tag "$design.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: path design diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 0ca6187c..47bc5157 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK { tag "$input_file" label 'process_single' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: path input_file diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf index 65cf9b95..3d6a99fa 100644 --- a/modules/local/sdrfparsing/main.nf +++ b/modules/local/sdrfparsing/main.nf @@ -2,10 +2,10 @@ process SDRFPARSING { tag "$sdrf.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: path sdrf diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf index 3035b4a9..7737539e 100644 --- a/modules/local/spectrum2features/main.nf +++ b/modules/local/spectrum2features/main.nf @@ -2,10 +2,10 @@ process SPECTRUM2FEATURES { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.16" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.16--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.16--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" input: tuple val(meta), path(id_file), path(ms_file) From 2338d1bf96a42044ec8868e828959fdb69bd0dc0 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 3 Dec 2024 16:55:43 +0000 Subject: [PATCH 4/8] replace quantms-utils 0.0.16 -> 0.0.17 --- modules/local/add_sage_feat/main.nf | 4 ++-- modules/local/diannconvert/main.nf | 4 ++-- modules/local/extract_psm/main.nf | 4 ++-- modules/local/extract_sample/main.nf | 4 ++-- modules/local/generate_diann_cfg/main.nf | 4 ++-- modules/local/mzmlstatistics/main.nf | 4 ++-- modules/local/preprocess_expdesign.nf | 4 ++-- modules/local/samplesheet_check.nf | 4 ++-- modules/local/sdrfparsing/main.nf | 4 ++-- modules/local/spectrum2features/main.nf | 4 ++-- 10 files changed, 20 insertions(+), 20 deletions(-) diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf index 6c014fde..fee0b605 100644 --- a/modules/local/add_sage_feat/main.nf +++ b/modules/local/add_sage_feat/main.nf @@ -4,8 +4,8 @@ process SAGEFEATURE { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: tuple val(meta), path(id_file), path(extra_feat) diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf index d3adbe8b..ae7582bf 100644 --- a/modules/local/diannconvert/main.nf +++ b/modules/local/diannconvert/main.nf @@ -4,8 +4,8 @@ process DIANNCONVERT { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: path(report) diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf index 68018636..93974a09 100644 --- a/modules/local/extract_psm/main.nf +++ b/modules/local/extract_psm/main.nf @@ -4,8 +4,8 @@ process PSMCONVERSION { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf index 5106f0ab..d470eb7b 100644 --- a/modules/local/extract_sample/main.nf +++ b/modules/local/extract_sample/main.nf @@ -4,8 +4,8 @@ process GETSAMPLE { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf index eb8209f1..2ea573ad 100644 --- a/modules/local/generate_diann_cfg/main.nf +++ b/modules/local/generate_diann_cfg/main.nf @@ -4,8 +4,8 @@ process GENERATE_DIANN_CFG { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: val(meta) diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf index 169d8789..3ff11be9 100644 --- a/modules/local/mzmlstatistics/main.nf +++ b/modules/local/mzmlstatistics/main.nf @@ -5,8 +5,8 @@ process MZMLSTATISTICS { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: tuple val(meta), path(ms_file) diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf index 03b066ba..29a91d10 100644 --- a/modules/local/preprocess_expdesign.nf +++ b/modules/local/preprocess_expdesign.nf @@ -8,8 +8,8 @@ process PREPROCESS_EXPDESIGN { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: path design diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 47bc5157..6f686a7c 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -5,8 +5,8 @@ process SAMPLESHEET_CHECK { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: path input_file diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf index 3d6a99fa..d760b49f 100644 --- a/modules/local/sdrfparsing/main.nf +++ b/modules/local/sdrfparsing/main.nf @@ -4,8 +4,8 @@ process SDRFPARSING { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: path sdrf diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf index 7737539e..3525c3e2 100644 --- a/modules/local/spectrum2features/main.nf +++ b/modules/local/spectrum2features/main.nf @@ -4,8 +4,8 @@ process SPECTRUM2FEATURES { conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: tuple val(meta), path(id_file), path(ms_file) From ae0b979f843f4a4d13262fc1f69b8d3bee84feb4 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Sun, 1 Dec 2024 07:29:48 +0000 Subject: [PATCH 5/8] replace quantms-utils 0.0.15 -> 0.0.17 --- modules/local/add_sage_feat/main.nf | 6 +++--- modules/local/diannconvert/main.nf | 6 +++--- modules/local/extract_psm/main.nf | 6 +++--- modules/local/extract_sample/main.nf | 6 +++--- modules/local/generate_diann_cfg/main.nf | 6 +++--- modules/local/ms2rescore/main.nf | 8 ++++---- modules/local/mzmlstatistics/main.nf | 6 +++--- modules/local/preprocess_expdesign.nf | 6 +++--- modules/local/samplesheet_check.nf | 6 +++--- modules/local/sdrfparsing/main.nf | 6 +++--- modules/local/spectrum2features/main.nf | 6 +++--- 11 files changed, 34 insertions(+), 34 deletions(-) diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf index 6acef0c4..fee0b605 100644 --- a/modules/local/add_sage_feat/main.nf +++ b/modules/local/add_sage_feat/main.nf @@ -2,10 +2,10 @@ process SAGEFEATURE { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: tuple val(meta), path(id_file), path(extra_feat) diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf index e8bdfd99..ae7582bf 100644 --- a/modules/local/diannconvert/main.nf +++ b/modules/local/diannconvert/main.nf @@ -2,10 +2,10 @@ process DIANNCONVERT { tag "$meta.experiment_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: path(report) diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf index 58899a54..93974a09 100644 --- a/modules/local/extract_psm/main.nf +++ b/modules/local/extract_psm/main.nf @@ -2,10 +2,10 @@ process PSMCONVERSION { tag "$meta.mzml_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf index 3a67e9e1..d470eb7b 100644 --- a/modules/local/extract_sample/main.nf +++ b/modules/local/extract_sample/main.nf @@ -2,10 +2,10 @@ process GETSAMPLE { tag "$design.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf index 768db3ae..2ea573ad 100644 --- a/modules/local/generate_diann_cfg/main.nf +++ b/modules/local/generate_diann_cfg/main.nf @@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG { tag "$meta.experiment_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: val(meta) diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf index e02a743f..49bb1cc4 100644 --- a/modules/local/ms2rescore/main.nf +++ b/modules/local/ms2rescore/main.nf @@ -2,10 +2,10 @@ process MS2RESCORE { tag "$meta.mzml_id" label 'process_high' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-rescoring=0.0.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.1--pyhdfd78af_0' : + 'biocontainers/quantms-rescoring:0.0.1--pyhdfd78af_0' }" // userEmulation settings when docker is specified containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : '' @@ -43,7 +43,7 @@ process MS2RESCORE { } """ - quantmsutilsc ms2rescore \\ + rescoring ms2rescore \\ --psm_file $idxml \\ --spectrum_path . \\ --ms2_tolerance $ms2_tolerence \\ diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf index 29918840..3ff11be9 100644 --- a/modules/local/mzmlstatistics/main.nf +++ b/modules/local/mzmlstatistics/main.nf @@ -3,10 +3,10 @@ process MZMLSTATISTICS { label 'process_very_low' label 'process_single' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: tuple val(meta), path(ms_file) diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf index 02937cb8..29a91d10 100644 --- a/modules/local/preprocess_expdesign.nf +++ b/modules/local/preprocess_expdesign.nf @@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN { tag "$design.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: path design diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index f7c46fbc..6f686a7c 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK { tag "$input_file" label 'process_single' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: path input_file diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf index 393c11e0..d760b49f 100644 --- a/modules/local/sdrfparsing/main.nf +++ b/modules/local/sdrfparsing/main.nf @@ -2,10 +2,10 @@ process SDRFPARSING { tag "$sdrf.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: path sdrf diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf index 27cbb4ee..3525c3e2 100644 --- a/modules/local/spectrum2features/main.nf +++ b/modules/local/spectrum2features/main.nf @@ -2,10 +2,10 @@ process SPECTRUM2FEATURES { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.15" + conda "bioconda::quantms-utils=0.0.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" input: tuple val(meta), path(id_file), path(ms_file) From 2d99f77354a5b1822dbba5148096bf524631b725 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Wed, 4 Dec 2024 06:14:10 +0000 Subject: [PATCH 6/8] replace quantms-utils 0.0.16 -> 0.0.17 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5fd09063..a1773c08 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -57,7 +57,7 @@ jobs: uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Set up Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@v3 with: version: "${{ matrix.NXF_VER }}" From a56de079825d7d0cbe41b749cbe03721781b1d8c Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Wed, 4 Dec 2024 06:15:57 +0000 Subject: [PATCH 7/8] replace quantms-utils 0.0.16 -> 0.0.17 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a1773c08..5fd09063 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -57,7 +57,7 @@ jobs: uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Set up Nextflow - uses: nf-core/setup-nextflow@v3 + uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" From 9f764adb1b76ed241c902c183df52c134df083cc Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Wed, 4 Dec 2024 06:21:24 +0000 Subject: [PATCH 8/8] minor fix CI java 17 --- .github/workflows/ci.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5fd09063..a14a8a72 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -56,6 +56,11 @@ jobs: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 + with: + distribution: "temurin" + java-version: "17" + - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 with: