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/CHANGELOG.md b/CHANGELOG.md index d618909534..8c963ffbc3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,24 @@ 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). +## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare + +Gällivare is a small lake next to Pierikjaure. + +### 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 +- [#1128](https://github.com/nf-core/sarek/pull/1128) - Prepare release `3.2.3` + +### 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. 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 2a8432ccf0..eb8c811ace 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' } @@ -323,7 +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 = '3.2.2' + version = '3.2.3' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 05e5a83c4f..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", @@ -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"],