From 7ccdb4f27f4f83de9c752ba6ef6d1f0c5b7e7c7a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 5 Jun 2023 18:07:05 +0200 Subject: [PATCH 01/14] back to dev --- CHANGELOG.md | 14 +++++++++++++- nextflow.config | 2 +- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6e1831f548..a38c1628a6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,18 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## dev + +### Added + +- [#1071](https://github.com/nf-core/sarek/pull/1071) - Back to dev + +### Changed + +### Fixed + +### Removed + ## [3.2.0](https://github.com/nf-core/sarek/releases/tag/3.2.0) - Bierikjávrre Bierikjávrre is one of the largest lake in Sarek. @@ -21,7 +33,7 @@ Bierikjávrre is one of the largest lake in Sarek. - [#978](https://github.com/nf-core/sarek/pull/978) - Validate that patient/sample does not contain spaces - [#981](https://github.com/nf-core/sarek/pull/981) - Added documentation on generating ASCAT resources for exome and targeted sequencing - [#1041](https://github.com/nf-core/sarek/pull/1041) - Add params `vep_custom_args` to let user specify custom params more easily for `VEP` -- [#1045](https://github.com/nf-core/sarek/pull/1045) - Add `public_aws_ecr` for using ECR hosted containers. +- [#1045](https://github.com/nf-core/sarek/pull/1045) - Add `public_aws_ecr` for using ECR hosted containers ### Changed diff --git a/nextflow.config b/nextflow.config index eeb4a10fc8..b5189ecf5d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -322,7 +322,7 @@ manifest { description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '3.2.0' + version = '3.3dev' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' } From 38ec0ec3b2cc8d221057ded5b484248bcd1d59da Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 5 Jun 2023 18:07:52 +0200 Subject: [PATCH 02/14] update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a38c1628a6..95f89562b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- [#1071](https://github.com/nf-core/sarek/pull/1071) - Back to dev +- [#1073](https://github.com/nf-core/sarek/pull/1073) - Back to dev ### Changed From fb849addd7caf66de41df0c053b9812ff1ebe3d4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 18:09:24 +0200 Subject: [PATCH 03/14] update tabix/bgziptabix --- modules.json | 2 +- modules/nf-core/tabix/bgziptabix/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index 8dbf98e633..e1f9fcede1 100644 --- a/modules.json +++ b/modules.json @@ -398,7 +398,7 @@ }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "01b3b2509d76625b6d6cd613b349fb4777712a15", + "git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e", "installed_by": ["vcf_annotate_snpeff", "modules"] }, "tabix/tabix": { diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index fef528fcdf..d6c5a760f3 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -5,7 +5,7 @@ process TABIX_BGZIPTABIX { conda "bioconda::tabix=1.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" + 'biocontainers/tabix:1.11--hdfd78af_0' }" input: tuple val(meta), path(input) From 6fe8f505287db8effc9467846c284ac8c0ae6280 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 18:10:51 +0200 Subject: [PATCH 04/14] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95f89562b6..706ff3ace1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo + ### Removed ## [3.2.0](https://github.com/nf-core/sarek/releases/tag/3.2.0) - Bierikjávrre From 1686e8c51b4c7e5cbef1d772bd51440f4557f543 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 18:17:41 +0200 Subject: [PATCH 05/14] fix typo in profile name --- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awsfulltest_germline.yml | 4 ++-- .github/workflows/awstest.yml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 84b2b282e4..bd4a18a7ef 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -25,7 +25,7 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test" } - profiles: test_full,public_aws_tower + profiles: test_full,public_aws_ecr - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/.github/workflows/awsfulltest_germline.yml b/.github/workflows/awsfulltest_germline.yml index f43848c827..0674c9297c 100644 --- a/.github/workflows/awsfulltest_germline.yml +++ b/.github/workflows/awsfulltest_germline.yml @@ -8,7 +8,7 @@ on: types: [published] workflow_dispatch: jobs: - run-tower-germline: + run-tower: name: Run AWS full tests if: github.repository == 'nf-core/sarek' runs-on: ubuntu-latest @@ -25,7 +25,7 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test" } - profiles: test_full_germline,aws_tower + profiles: test_full_germline,public_aws_ecr - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 6d7751e3d1..d1c521fd7f 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -22,7 +22,7 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}" } - profiles: test,public_aws_tower + profiles: test,public_aws_ecr - uses: actions/upload-artifact@v3 with: name: Tower debug log file From 2243243afff8afda85398a79b0d4f697ea35f139 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 18:32:03 +0200 Subject: [PATCH 06/14] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 706ff3ace1..7a9e5eb33a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed - [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo +- [#1079](https://github.com/nf-core/sarek/pull/1045) - Fixed typo in profile name for tower aws megatests ### Removed From 1e24fe232d24dd86db3913535a220f9b8062e16d Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 7 Jun 2023 18:35:26 +0200 Subject: [PATCH 07/14] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a9e5eb33a..60dc60793a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed - [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo +- [#1079](https://github.com/nf-core/sarek/pull/1079) - Fixed typo in profile name for tower aws megatests - [#1079](https://github.com/nf-core/sarek/pull/1045) - Fixed typo in profile name for tower aws megatests ### Removed From 2ad1282347556c49db540174667b6a84389ba3d8 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 7 Jun 2023 18:35:51 +0200 Subject: [PATCH 08/14] Update CHANGELOG.md --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 60dc60793a..e7ce2944c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo - [#1079](https://github.com/nf-core/sarek/pull/1079) - Fixed typo in profile name for tower aws megatests -- [#1079](https://github.com/nf-core/sarek/pull/1045) - Fixed typo in profile name for tower aws megatests ### Removed From c7dcfe2cddf84df02df7f2ddbbc7b4818da30781 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 18:44:43 +0200 Subject: [PATCH 09/14] prepare release 3.2.1 --- CHANGELOG.md | 11 +++++------ nextflow.config | 2 +- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95f89562b6..b438904370 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,17 +5,16 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## dev +## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure -### Added - -- [#1073](https://github.com/nf-core/sarek/pull/1073) - Back to dev +Pierikjaure is a previous spelling of Bierikjávrre. ### Changed -### Fixed +- [#1073](https://github.com/nf-core/sarek/pull/1073) - Back to dev +- [#1080](https://github.com/nf-core/sarek/pull/1080) - Prepare release `3.2.1` -### Removed +### Fixed ## [3.2.0](https://github.com/nf-core/sarek/releases/tag/3.2.0) - Bierikjávrre diff --git a/nextflow.config b/nextflow.config index b5189ecf5d..6ebf0db79b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -322,7 +322,7 @@ manifest { description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '3.3dev' + version = '3.2.1' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' } From bc1985b1e6e3dd1a7ec1256df8327ee0b89f4b5a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 19:31:08 +0200 Subject: [PATCH 10/14] patch more modules --- CHANGELOG.md | 2 ++ modules.json | 10 +++++----- modules/nf-core/deepvariant/main.nf | 2 +- modules/nf-core/gatk4/applybqsrspark/main.nf | 2 +- modules/nf-core/gatk4/baserecalibratorspark/main.nf | 2 +- modules/nf-core/gatk4/cnnscorevariants/main.nf | 2 +- modules/nf-core/gatk4/markduplicatesspark/main.nf | 2 +- 7 files changed, 12 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95f89562b6..657580cce7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- [#1082](https://github.com/nf-core/sarek/pull/1082) - Patch more modules to use quay.io registry + ### Removed ## [3.2.0](https://github.com/nf-core/sarek/releases/tag/3.2.0) - Bierikjávrre diff --git a/modules.json b/modules.json index 8dbf98e633..ede849ff9d 100644 --- a/modules.json +++ b/modules.json @@ -107,7 +107,7 @@ }, "deepvariant": { "branch": "master", - "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "dragmap/align": { @@ -168,7 +168,7 @@ }, "gatk4/applybqsrspark": { "branch": "master", - "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "gatk4/applyvqsr": { @@ -183,7 +183,7 @@ }, "gatk4/baserecalibratorspark": { "branch": "master", - "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "gatk4/calculatecontamination": { @@ -193,7 +193,7 @@ }, "gatk4/cnnscorevariants": { "branch": "master", - "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { @@ -263,7 +263,7 @@ }, "gatk4/markduplicatesspark": { "branch": "master", - "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "gatk4/mergemutectstats": { diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf index 2cea90ab9b..1a24ba34b8 100644 --- a/modules/nf-core/deepvariant/main.nf +++ b/modules/nf-core/deepvariant/main.nf @@ -2,7 +2,7 @@ process DEEPVARIANT { tag "$meta.id" label 'process_high' - container "docker.io/google/deepvariant:1.5.0" + container "nf-core/deepvariant:1.5.0" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/nf-core/gatk4/applybqsrspark/main.nf b/modules/nf-core/gatk4/applybqsrspark/main.nf index e920a2554d..88ead471c8 100644 --- a/modules/nf-core/gatk4/applybqsrspark/main.nf +++ b/modules/nf-core/gatk4/applybqsrspark/main.nf @@ -3,7 +3,7 @@ process GATK4_APPLYBQSR_SPARK { label 'process_low' conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" - container 'docker.io/broadinstitute/gatk:4.4.0.0' + container "nf-core/gatk:4.4.0.0" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/baserecalibratorspark/main.nf b/modules/nf-core/gatk4/baserecalibratorspark/main.nf index 8857dbc382..d240a10d3f 100644 --- a/modules/nf-core/gatk4/baserecalibratorspark/main.nf +++ b/modules/nf-core/gatk4/baserecalibratorspark/main.nf @@ -3,7 +3,7 @@ process GATK4_BASERECALIBRATOR_SPARK { label 'process_low' conda "bioconda::gatk4=4.4.0.0 conda-forge::openjdk=8.0.312" - container 'docker.io/broadinstitute/gatk:4.4.0.0' + container "nf-core/gatk:4.4.0.0" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf index 730544f61e..5e843ce6c6 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -3,7 +3,7 @@ process GATK4_CNNSCOREVARIANTS { label 'process_low' //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "docker.io/broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package + container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/nf-core/gatk4/markduplicatesspark/main.nf b/modules/nf-core/gatk4/markduplicatesspark/main.nf index d1388298c1..f64fbfd521 100644 --- a/modules/nf-core/gatk4/markduplicatesspark/main.nf +++ b/modules/nf-core/gatk4/markduplicatesspark/main.nf @@ -3,7 +3,7 @@ process GATK4_MARKDUPLICATES_SPARK { label 'process_high' conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" - container 'docker.io/broadinstitute/gatk:4.4.0.0' + container "nf-core/gatk:4.4.0.0" input: tuple val(meta), path(bam) From 87480b2a95b45e2bdf48e5160268f6e804aee9a9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 19:58:35 +0200 Subject: [PATCH 11/14] prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c20b8bb7ec..b29051f702 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ Pierikjaure is a previous spelling of Bierikjávrre. - [#1080](https://github.com/nf-core/sarek/pull/1080) - Prepare release `3.2.1` ### Fixed + - [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo - [#1079](https://github.com/nf-core/sarek/pull/1079) - Fixed typo in profile name for tower aws megatests From 382b1f925a97c8c2c1390ff1dfd29f895dbb2f22 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 20:43:37 +0200 Subject: [PATCH 12/14] update public _aws_ecr profile --- CHANGELOG.md | 1 + conf/public_aws_ecr.config | 15 +++++++++++++++ 2 files changed, 16 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3a4453d3a5..02f17472a4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo - [#1079](https://github.com/nf-core/sarek/pull/1079) - Fixed typo in profile name for tower aws megatests - [#1082](https://github.com/nf-core/sarek/pull/1082) - Patch more modules to use quay.io registry +- [#1082](https://github.com/nf-core/sarek/pull/1082) - Update `public_aws_ecr` profile ### Removed diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config index a1445ebed8..335909060a 100644 --- a/conf/public_aws_ecr.config +++ b/conf/public_aws_ecr.config @@ -39,9 +39,24 @@ process { withName: 'CREATE_INTERVALS_BED' { container = 'quay.io/biocontainers/gawk:5.1.0' } + withName: 'DEEPVARIANT' { + container = 'quay.io/nf-core/deepvariant:1.5.0' + } withName: 'DRAGMAP_ALIGN' { container = 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' } + withName: 'GATK4_APPLYBQSR_SPARK' { + container = 'quay.io/nf-core/gatk:4.4.0.0' + } + withName: 'GATK4_BASERECALIBRATOR_SPARK' { + container = 'quay.io/nf-core/gatk:4.4.0.0' + } + withName: 'GATK4_CNNSCOREVARIANTS' { + container = 'quay.io/nf-core/gatk:4.4.0.0' + } + withName: 'GATK4_MARKDUPLICATES_SPARK' { + container = 'quay.io/nf-core/gatk:4.4.0.0' + } withName: 'SAMBLASTER' { container = 'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:cee56b506ceb753d4bbef7e05b81e1bfc25d937f-0' } From 0952e294cb36d58fd68377f516c9729b503ca2be Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 21:18:52 +0200 Subject: [PATCH 13/14] add registry for singularity --- CHANGELOG.md | 1 + nextflow.config | 9 +++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 02f17472a4..abfff0b662 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1079](https://github.com/nf-core/sarek/pull/1079) - Fixed typo in profile name for tower aws megatests - [#1082](https://github.com/nf-core/sarek/pull/1082) - Patch more modules to use quay.io registry - [#1082](https://github.com/nf-core/sarek/pull/1082) - Update `public_aws_ecr` profile +- [#1082](https://github.com/nf-core/sarek/pull/1082) - Add quay.io as singularity default registry ### Removed diff --git a/nextflow.config b/nextflow.config index b5189ecf5d..204f94ce6d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -291,11 +291,12 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] -// Set default registry for Docker and Podman independent of -profile -// Will not be used unless Docker / Podman are enabled +// Set default registry for Docker, Singularity and Podman independent of -profile +// Will not be used unless Docker, Singularity and Podman are enabled // Set to your registry if you have a mirror of containers -docker.registry = 'quay.io' -podman.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { From 3bcc1040a1023286e115298313acea20376d31ce Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 22:00:16 +0200 Subject: [PATCH 14/14] nf-core bump-version -n 23.04.0 --- .github/workflows/ci.yml | 2 +- .github/workflows/pytest-workflow.yml | 2 +- CHANGELOG.md | 2 ++ README.md | 2 +- nextflow.config | 2 +- 5 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b97b8b5d63..743876c1eb 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" test: - "default" diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 8b6f9d2ccc..394802985f 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -37,7 +37,7 @@ jobs: TEST_DATA_BASE: - "test-datasets/data" NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" exclude: # - profile: "conda" diff --git a/CHANGELOG.md b/CHANGELOG.md index abfff0b662..2d8c95a74a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- [#1082](https://github.com/nf-core/sarek/pull/1082) - Bump minimal Nextflow version to 23.04.0 + ### Fixed - [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo diff --git a/README.md b/README.md index eba6b6ab2f..370f3557a8 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/sarek/results) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3476426-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3476425) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/nextflow.config b/nextflow.config index 204f94ce6d..dafabcfca1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -322,7 +322,7 @@ manifest { homePage = 'https://github.com/nf-core/sarek' description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' version = '3.3dev' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' }