From df493dfcdfc416038cde426289d0de1b64c8a95b Mon Sep 17 00:00:00 2001 From: asp8200 Date: Thu, 15 Jun 2023 15:22:17 +0000 Subject: [PATCH 1/7] back to dev --- CHANGELOG.md | 10 ++++++++++ nextflow.config | 2 +- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d618909534..c251401f6b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +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 + +### Added + +- [#1112](https://github.com/nf-core/sarek/pull/1112) - Back to dev + +### Changed + +### Fixed + ## [3.2.2](https://github.com/nf-core/sarek/releases/tag/3.2.2) - Vuoinesluobbalah Vuoinesluobbalah is a lake close to Bierikjávrre. diff --git a/nextflow.config b/nextflow.config index 2a8432ccf0..f94154dd0b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -323,7 +323,7 @@ manifest { description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.2.2' + version = '3.3dev' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' } From a8ed7e87b1c9291375f60cae67fef4ce1c2ad402 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Jun 2023 10:29:03 +0200 Subject: [PATCH 2/7] remove public_aws_ecr --- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awsfulltest_germline.yml | 2 +- .github/workflows/awstest.yml | 2 +- conf/public_aws_ecr.config | 73 ---------------------- nextflow.config | 3 - 5 files changed, 3 insertions(+), 79 deletions(-) delete mode 100644 conf/public_aws_ecr.config diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 9a41b26a0e..401222be25 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -26,7 +26,7 @@ jobs: "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test" } - profiles: test_full,public_aws_ecr + profiles: test_full - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/.github/workflows/awsfulltest_germline.yml b/.github/workflows/awsfulltest_germline.yml index 0e9867e4f2..bd9cf6c342 100644 --- a/.github/workflows/awsfulltest_germline.yml +++ b/.github/workflows/awsfulltest_germline.yml @@ -26,7 +26,7 @@ jobs: "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test" } - profiles: test_full_germline,public_aws_ecr + profiles: test_full_germline - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index d1c521fd7f..ae40b9538f 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_ecr + profiles: test - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config deleted file mode 100644 index 75ff69f723..0000000000 --- a/conf/public_aws_ecr.config +++ /dev/null @@ -1,73 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - AWS ECR Config -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config to set public AWS ECR images wherever possible - This improves speed when running on AWS infrastructure. - Use this as an example template when using your own private registry. ----------------------------------------------------------------------------------------- -*/ - -docker.registry = 'public.ecr.aws' -podman.registry = 'public.ecr.aws' -singularity.registry = 'public.ecr.aws' - -process { - withName: 'ADD_INFO_TO_VCF' { - container = 'quay.io/biocontainers/gawk:5.1.0' - } - withName: 'ASCAT' { - container = 'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:ba3e6d2157eac2d38d22e62ec87675e12adb1010-0' - } - withName: 'BUILD_INTERVALS' { - container = 'quay.io/biocontainers/gawk:5.1.0' - } - withName: 'BWAMEM2_MEM' { - container = 'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' - } - withName: 'BWA_MEM' { - container = 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' - } - withName: 'CAT_CAT' { - container = 'quay.io/biocontainers/pigz:2.3.4' - } - withName: 'CAT_FASTQ' { - container = 'quay.io/nf-core/ubuntu:20.04' - } - withName: 'CNVKIT_BATCH' { - container = 'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' - } - 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' - } - withName: 'SVDB_MERGE' { - container = 'quay.io/biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:af6f8534cd538a85ff43a2eae1b52b143e7abd05-0' - } - withName: 'UNTAR' { - container = 'quay.io/nf-core/ubuntu:20.04' - } - withName: 'UNZIP' { - container = 'quay.io/biocontainers/p7zip:16.02' - } -} diff --git a/nextflow.config b/nextflow.config index f94154dd0b..728c73c44a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -234,9 +234,6 @@ profiles { executor.memory = 60.GB executor.name = 'local' } - public_aws_ecr { - includeConfig 'conf/public_aws_ecr.config' - } // Basic test profile for CI test { includeConfig 'conf/test.config' } test_cache { includeConfig 'conf/test/cache.config' } From db59f4974ddf9d38e1bab89c3c409bf5d9243f78 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Jun 2023 12:06:23 +0200 Subject: [PATCH 3/7] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c251401f6b..f4588b67be 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 +- [#1118](https://github.com/nf-core/sarek/pull/1118) - Remove `public_aws_ecr` profile + ## [3.2.2](https://github.com/nf-core/sarek/releases/tag/3.2.2) - Vuoinesluobbalah Vuoinesluobbalah is a lake close to Bierikjávrre. From 5acab8e775c3d760fbb3d74f6aabac5657f9a45b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Jun 2023 13:59:11 +0200 Subject: [PATCH 4/7] remove default = null from schema --- nextflow_schema.json | 2 -- 1 file changed, 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 05e5a83c4f..d13c7f2a88 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -345,7 +345,6 @@ }, "cnvkit_reference": { "type": "string", - "default": null, "fa_icon": "fas fa-file", "help_text": "https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=reference.cnn#batch", "description": "Copy-number reference for CNVkit", @@ -528,7 +527,6 @@ "ascat_genome": { "type": "string", "fa_icon": "fa-solid fa-text", - "default": null, "description": "ASCAT genome.", "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\n\nMust be set to run ASCAT, either hg19 or hg38. If you use AWS iGenomes, this has already been set for you appropriately.", "enum": ["None", "hg19", "hg38"], From 0c1770a681778ba62a250c3aec1e2d0129e1c240 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Jun 2023 14:06:35 +0200 Subject: [PATCH 5/7] add help_text for input_output_options --- nextflow_schema.json | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index d13c7f2a88..f2aeadbea8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,8 +10,19 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", + "help_text": "Specify input samplesheet, step and output folder.", "required": ["step", "outdir"], "properties": { + "input": { + "type": "string", + "format": "file-path", + "mimetype": "text/csv", + "pattern": "^\\S+\\.csv$", + "schema": "assets/schema_input.json", + "description": "Path to comma-separated file containing information about the samples in the experiment.", + "help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).\n\nIf no input file is specified, sarek will attempt to locate one in the `{outdir}` directory.", + "fa_icon": "fas fa-file-csv" + }, "step": { "type": "string", "default": "mapping", @@ -27,24 +38,13 @@ "annotate" ] }, - "input": { - "type": "string", - "format": "file-path", - "mimetype": "text/csv", - "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", - "description": "Path to comma-separated file containing information about the samples in the experiment.", - "help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).\n\nIf no input file is specified, sarek will attempt to locate one in the `{outdir}` directory.", - "fa_icon": "fas fa-file-csv" - }, "outdir": { "type": "string", "format": "directory-path", "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open" } - }, - "help_text": "" + } }, "main_options": { "title": "Main options", From 6e638e475d9ca625756008e7d3844603990985cb Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Jun 2023 14:07:44 +0200 Subject: [PATCH 6/7] update CHANGELOG --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c251401f6b..67874f1f18 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,9 +10,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - [#1112](https://github.com/nf-core/sarek/pull/1112) - Back to dev +- [#1119](https://github.com/nf-core/sarek/pull/1119) - Added `help_text` for `input_output_options` group in schema ### Changed +- [#1119](https://github.com/nf-core/sarek/pull/1119) - Remove `null` by default in schema + ### Fixed ## [3.2.2](https://github.com/nf-core/sarek/releases/tag/3.2.2) - Vuoinesluobbalah From f41babfc7a4b3fb8eb863faf05e7b1790e194d86 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen Date: Thu, 22 Jun 2023 12:05:14 +0200 Subject: [PATCH 7/7] prepare 3.2.3 --- CHANGELOG.md | 5 ++++- nextflow.config | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 391228a5f6..8c963ffbc3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,9 @@ 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 +## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare + +Gällivare is a small lake next to Pierikjaure. ### Added @@ -15,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - [#1119](https://github.com/nf-core/sarek/pull/1119) - Remove `null` by default in schema +- [#1128](https://github.com/nf-core/sarek/pull/1128) - Prepare release `3.2.3` ### Fixed diff --git a/nextflow.config b/nextflow.config index 728c73c44a..eb8c811ace 100644 --- a/nextflow.config +++ b/nextflow.config @@ -320,7 +320,7 @@ manifest { description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.3dev' + version = '3.2.3' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' }