From 5fe5cdff171e3baed603b3990cab7f7fd3fcb992 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 18 Feb 2025 09:44:52 +0100 Subject: [PATCH 01/11] Release 3.5.1 (#1799) ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors). --------- Co-authored-by: Friederike Hanssen Co-authored-by: Friederike Hanssen Co-authored-by: tdanhorn Co-authored-by: Thomas --- .github/workflows/cloudtest.yml | 27 ++++++++++------ CHANGELOG.md | 31 +++++++++++++++++++ assets/multiqc_config.yml | 12 ++++--- conf/modules/joint_germline.config | 4 ++- nextflow.config | 20 ++++++------ nextflow_schema.json | 4 +-- tests/aligner-bwa-mem.nf.test.snap | 4 +-- tests/aligner-bwa-mem2.nf.test.snap | 4 +-- tests/aligner-dragmap.nf.test.snap | 4 +-- tests/alignment_from_everything.nf.test.snap | 2 +- tests/alignment_to_fastq.nf.test.snap | 2 +- tests/annotation_bcfann.nf.test.snap | 2 +- tests/annotation_merge.nf.test.snap | 4 +-- tests/annotation_snpeff.nf.test.snap | 2 +- tests/annotation_vep.nf.test.snap | 2 +- tests/default.nf.test.snap | 2 +- tests/save_output_as_bam.nf.test.snap | 2 +- tests/saved_mapped.nf.test.snap | 2 +- tests/sentieon.nf.test.snap | 2 +- tests/start_from_markduplicates.nf.test.snap | 8 ++--- ...art_from_preparerecalibration.nf.test.snap | 8 ++--- tests/start_from_recalibration.nf.test.snap | 8 ++--- tests/tumor-normal-pair.nf.test.snap | 2 +- .../variant_calling_controlfreec.nf.test.snap | 12 +++---- tests/variant_calling_strelka.nf.test.snap | 10 +++--- tests/variant_calling_strelka_bp.nf.test.snap | 4 +-- 26 files changed, 114 insertions(+), 70 deletions(-) diff --git a/.github/workflows/cloudtest.yml b/.github/workflows/cloudtest.yml index 932951b07c..1015130875 100644 --- a/.github/workflows/cloudtest.yml +++ b/.github/workflows/cloudtest.yml @@ -81,13 +81,24 @@ jobs: if: github.repository == 'nf-core/sarek' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: - - uses: octokit/request-action@v2.x + - name: Get PR reviews + uses: octokit/request-action@v2.x + if: github.event_name != 'workflow_dispatch' id: check_approvals + continue-on-error: true with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - id: test_variables + + - name: Check for approvals + if: ${{ failure() && github.event_name != 'workflow_dispatch' }} + run: | + echo "No review approvals found. At least 2 approvals are required to run this action automatically." + exit 1 + + - name: Check for enough approvals (>=2) + id: test_variables if: github.event_name != 'workflow_dispatch' run: | JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' @@ -114,11 +125,9 @@ jobs: } profiles: ${{ matrix.profile }} - - uses: actions/upload-artifact@v3 - name: Save Logs - if: success() || failure() + - uses: actions/upload-artifact@v4 with: - name: tower-${{ matrix.profile }}-log + name: Seqera Platform debug log file path: | - tower_action_*.log - tower_action_*.json + seqera_platform_action_*.log + seqera_platform_action_*.json diff --git a/CHANGELOG.md b/CHANGELOG.md index 4e90ea7cac..b9e1102a16 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,37 @@ 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). +## [3.5.1](https://github.com/nf-core/sarek/releases/tag/3.5.1) - Akkatjåkkå + +Akkatjåkkå is another glacier. + +### Added + +- [1759](https://github.com/nf-core/sarek/pull/1759) - Back to dev + +### Changed + +- [1767](https://github.com/nf-core/sarek/pull/1767) - Bump nf-schema version to 2.2.1 +- [1777](https://github.com/nf-core/sarek/pull/1777) - Merge intervals for WES in GATK GenomicsDBImport +- [1798](https://github.com/nf-core/sarek/pull/1798) - Prepare release 3.5.1 + +### Fixed + +- [1797](https://github.com/nf-core/sarek/pull/1797) - Use `file-path-pattern` over `file-path` to hanlde glob for `known_indels` and `known_indels_tbi` to fix [1785](https://github.com/nf-core/sarek/issues/1785) +- [1802](https://github.com/nf-core/sarek/pull/1802) - Update GHA for full_test tests + +### Removed + +### Dependencies + +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | + +### Parameters + +| Params | Status | +| ------ | ------ | + ## [3.5.0](https://github.com/nf-core/sarek/releases/tag/3.5.0) - Áhkájiegna A set of connecting glaciers. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 4165fec686..8e69d3605c 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,10 @@ custom_logo_url: https://github.com/nf-core/sarek/ custom_logo_title: "nf-core/sarek" report_comment: > - This report has been generated by the nf-core/sarek - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/sarek analysis pipeline. For information about how to + interpret these results, please see the documentation. report_section_order: "nf-core-sarek-methods-description": order: -1000 @@ -41,7 +42,8 @@ module_order: name: "FastP (Read preprocessing)" - picard: name: "GATK4 MarkDuplicates" - info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity (with --use_gatk_spark)." + info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity + (with --use_gatk_spark)." - samtools: name: "Samtools Flagstat" - mosdepth: @@ -63,7 +65,7 @@ extra_fn_clean_exts: pattern: "^.*.(md|recal).mosdepth.(global|region).dist" module: mosdepth -sample_names_replace_regex: True +sample_names_replace_regex: true sample_names_replace: "\\.[0-9]{4}$": ".md" # should match ".0001" but only at the end of strings for module Markduplicates/EstimateLibraryComplexity module: picard diff --git a/conf/modules/joint_germline.config b/conf/modules/joint_germline.config index 61a296721d..b3f5bffc8b 100644 --- a/conf/modules/joint_germline.config +++ b/conf/modules/joint_germline.config @@ -16,7 +16,9 @@ process { withName: 'GATK4_GENOMICSDBIMPORT' { - ext.args = { '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' } + ext.args = { params.wes ? + '--merge-input-intervals --genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' : + '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' } ext.prefix = { "${meta.intervals_name}.joint" } publishDir = [ enabled: false diff --git a/nextflow.config b/nextflow.config index 1268aab63a..d1ce54b291 100644 --- a/nextflow.config +++ b/nextflow.config @@ -336,14 +336,14 @@ env { } // Set bash options -process.shell = """\ -bash - -set -e # Exit if a tool returns a non-zero status/exit code -set -u # Treat unset variables and parameters as an error -set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute -set -C # No clobber - prevent output redirection from overwriting files. -""" +process.shell = [ + "bash", + "-C", // No clobber - prevent output redirection from overwriting files. + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o", // Returns the status of the last command to exit.. + "pipefail" // ..with a non-zero status or zero if all successfully execute +] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -381,13 +381,13 @@ manifest { description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '3.5.0' + version = '3.5.1' doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' } // Nextflow plugins plugins { - id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.2.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet id 'nf-prov@1.2.2' // Provenance reports for pipeline runs } diff --git a/nextflow_schema.json b/nextflow_schema.json index 5cdf35d555..e5dc346c24 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -706,7 +706,7 @@ "known_indels": { "type": "string", "fa_icon": "fas fa-copy", - "format": "file-path", + "format": "file-path-pattern", "exists": true, "mimetype": "text/plain", "description": "Path to known indels file.", @@ -715,7 +715,7 @@ "known_indels_tbi": { "type": "string", "fa_icon": "fas fa-copy", - "format": "file-path", + "format": "file-path-pattern", "exists": true, "mimetype": "text/plain", "description": "Path to known indels file index.", diff --git a/tests/aligner-bwa-mem.nf.test.snap b/tests/aligner-bwa-mem.nf.test.snap index 9744bcceef..b4360c538f 100644 --- a/tests/aligner-bwa-mem.nf.test.snap +++ b/tests/aligner-bwa-mem.nf.test.snap @@ -17,7 +17,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -72,7 +72,7 @@ 5, { "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/aligner-bwa-mem2.nf.test.snap b/tests/aligner-bwa-mem2.nf.test.snap index 5ab17312a0..4d6bfbd085 100644 --- a/tests/aligner-bwa-mem2.nf.test.snap +++ b/tests/aligner-bwa-mem2.nf.test.snap @@ -4,7 +4,7 @@ 5, { "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -60,7 +60,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/aligner-dragmap.nf.test.snap b/tests/aligner-dragmap.nf.test.snap index 3302761f2d..8104e4158e 100644 --- a/tests/aligner-dragmap.nf.test.snap +++ b/tests/aligner-dragmap.nf.test.snap @@ -4,7 +4,7 @@ 5, { "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -64,7 +64,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/alignment_from_everything.nf.test.snap b/tests/alignment_from_everything.nf.test.snap index b82b7fbb11..c709f34f7e 100644 --- a/tests/alignment_from_everything.nf.test.snap +++ b/tests/alignment_from_everything.nf.test.snap @@ -51,7 +51,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/alignment_to_fastq.nf.test.snap b/tests/alignment_to_fastq.nf.test.snap index 53a0512f82..abb5b18d53 100644 --- a/tests/alignment_to_fastq.nf.test.snap +++ b/tests/alignment_to_fastq.nf.test.snap @@ -51,7 +51,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/annotation_bcfann.nf.test.snap b/tests/annotation_bcfann.nf.test.snap index 0aa7d675ce..4ad6ab7316 100644 --- a/tests/annotation_bcfann.nf.test.snap +++ b/tests/annotation_bcfann.nf.test.snap @@ -7,7 +7,7 @@ "bcftools": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/annotation_merge.nf.test.snap b/tests/annotation_merge.nf.test.snap index 62ea3b6aca..75fde8c984 100644 --- a/tests/annotation_merge.nf.test.snap +++ b/tests/annotation_merge.nf.test.snap @@ -16,7 +16,7 @@ "tabix": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -122,7 +122,7 @@ "tabix": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/annotation_snpeff.nf.test.snap b/tests/annotation_snpeff.nf.test.snap index da7ef2d016..eb236d9baf 100644 --- a/tests/annotation_snpeff.nf.test.snap +++ b/tests/annotation_snpeff.nf.test.snap @@ -10,7 +10,7 @@ "tabix": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/annotation_vep.nf.test.snap b/tests/annotation_vep.nf.test.snap index d9d82cda3d..8d8a8c710f 100644 --- a/tests/annotation_vep.nf.test.snap +++ b/tests/annotation_vep.nf.test.snap @@ -10,7 +10,7 @@ "tabix": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5bf1b26c5e..05c09b6f1a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -39,7 +39,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/save_output_as_bam.nf.test.snap b/tests/save_output_as_bam.nf.test.snap index 55f6083979..14be38aa2f 100644 --- a/tests/save_output_as_bam.nf.test.snap +++ b/tests/save_output_as_bam.nf.test.snap @@ -17,7 +17,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/saved_mapped.nf.test.snap b/tests/saved_mapped.nf.test.snap index 987f214d70..da7f368c6d 100644 --- a/tests/saved_mapped.nf.test.snap +++ b/tests/saved_mapped.nf.test.snap @@ -17,7 +17,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/sentieon.nf.test.snap b/tests/sentieon.nf.test.snap index 4c66400e96..42e489fbc3 100644 --- a/tests/sentieon.nf.test.snap +++ b/tests/sentieon.nf.test.snap @@ -39,7 +39,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/start_from_markduplicates.nf.test.snap b/tests/start_from_markduplicates.nf.test.snap index def63ca189..05ee60a899 100644 --- a/tests/start_from_markduplicates.nf.test.snap +++ b/tests/start_from_markduplicates.nf.test.snap @@ -16,7 +16,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -148,7 +148,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -323,7 +323,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -475,7 +475,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/start_from_preparerecalibration.nf.test.snap b/tests/start_from_preparerecalibration.nf.test.snap index bfaab47657..dbbebfddea 100644 --- a/tests/start_from_preparerecalibration.nf.test.snap +++ b/tests/start_from_preparerecalibration.nf.test.snap @@ -10,7 +10,7 @@ "gatk4": "4.5.0.0" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -78,7 +78,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -196,7 +196,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -314,7 +314,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/start_from_recalibration.nf.test.snap b/tests/start_from_recalibration.nf.test.snap index b07d2def0c..2b42f75e2e 100644 --- a/tests/start_from_recalibration.nf.test.snap +++ b/tests/start_from_recalibration.nf.test.snap @@ -10,7 +10,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -80,7 +80,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -198,7 +198,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -310,7 +310,7 @@ "gatk4": "4.5.0.0" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap index 92aef2e017..b6f35684b3 100644 --- a/tests/tumor-normal-pair.nf.test.snap +++ b/tests/tumor-normal-pair.nf.test.snap @@ -42,7 +42,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/variant_calling_controlfreec.nf.test.snap b/tests/variant_calling_controlfreec.nf.test.snap index f468d84f5c..e7932a0093 100644 --- a/tests/variant_calling_controlfreec.nf.test.snap +++ b/tests/variant_calling_controlfreec.nf.test.snap @@ -7,7 +7,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -75,7 +75,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -162,7 +162,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -302,7 +302,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -424,7 +424,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -533,7 +533,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap index c72841c0f2..0943c3ec67 100644 --- a/tests/variant_calling_strelka.nf.test.snap +++ b/tests/variant_calling_strelka.nf.test.snap @@ -16,7 +16,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -221,7 +221,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -401,7 +401,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -575,7 +575,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -709,7 +709,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ diff --git a/tests/variant_calling_strelka_bp.nf.test.snap b/tests/variant_calling_strelka_bp.nf.test.snap index 7a773f06ec..aca20ac139 100644 --- a/tests/variant_calling_strelka_bp.nf.test.snap +++ b/tests/variant_calling_strelka_bp.nf.test.snap @@ -22,7 +22,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ @@ -244,7 +244,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.5.1" } }, [ From 0d7c46e8b8a7f355c68a73d763ca1782d174bf6f Mon Sep 17 00:00:00 2001 From: John Orgera Date: Tue, 18 Mar 2025 10:48:11 -0400 Subject: [PATCH 02/11] applybqsr updated --- modules.json | 440 +++++++++++++----- .../gatk4spark/applybqsr/environment.yml | 4 +- modules/nf-core/gatk4spark/applybqsr/main.nf | 12 +- modules/nf-core/gatk4spark/applybqsr/meta.yml | 160 ++++--- .../applybqsr/tests/main.nf.test.snap | 40 +- 5 files changed, 442 insertions(+), 214 deletions(-) diff --git a/modules.json b/modules.json index 12adb8c51e..2fe818ef4f 100644 --- a/modules.json +++ b/modules.json @@ -8,517 +8,725 @@ "ascat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/annotate": { "branch": "master", "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/mpileup": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["bam_ngscheckmate"] + "installed_by": [ + "bam_ngscheckmate" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/stats": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - 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"installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/merge": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": ["modules", "vcf_annotate_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_snpeff" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": ["modules", "vcf_annotate_ensemblvep"] + "installed_by": [ + "modules", + "vcf_annotate_ensemblvep" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "unzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcftools": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -527,35 +735,47 @@ "bam_ngscheckmate": { "branch": "master", "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_ensemblvep": { "branch": "master", "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/gatk4spark/applybqsr/environment.yml b/modules/nf-core/gatk4spark/applybqsr/environment.yml index 14075a574a..a5c49e9557 100644 --- a/modules/nf-core/gatk4spark/applybqsr/environment.yml +++ b/modules/nf-core/gatk4spark/applybqsr/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4-spark=4.5.0.0 + - bioconda::gatk4-spark=4.6.1.0 diff --git a/modules/nf-core/gatk4spark/applybqsr/main.nf b/modules/nf-core/gatk4spark/applybqsr/main.nf index 316ddc0b1d..abd4c9946e 100644 --- a/modules/nf-core/gatk4spark/applybqsr/main.nf +++ b/modules/nf-core/gatk4spark/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4SPARK_APPLYBQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.5.0.0--hdfd78af_0': - 'biocontainers/gatk4-spark:4.5.0.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) @@ -14,8 +14,8 @@ process GATK4SPARK_APPLYBQSR { path dict output: - tuple val(meta), path("*.bam") , emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("${prefix}.bam") , emit: bam, optional: true + tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true path "versions.yml" , emit: versions when: @@ -23,7 +23,7 @@ process GATK4SPARK_APPLYBQSR { script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def interval_command = intervals ? "--intervals $intervals" : "" def avail_mem = 3072 @@ -52,7 +52,7 @@ process GATK4SPARK_APPLYBQSR { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bam touch ${prefix}.cram diff --git a/modules/nf-core/gatk4spark/applybqsr/meta.yml b/modules/nf-core/gatk4spark/applybqsr/meta.yml index 609af2f450..909be9276a 100644 --- a/modules/nf-core/gatk4spark/applybqsr/meta.yml +++ b/modules/nf-core/gatk4spark/applybqsr/meta.yml @@ -1,85 +1,91 @@ name: gatk4spark_applybqsr description: Apply base quality score recalibration (BQSR) to a bam file keywords: - - bam - - base quality score recalibration - - bqsr - - cram - - gatk4spark +- bam +- base quality score recalibration +- bqsr +- cram +- gatk4spark tools: - - gatk4: - description: | - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. - homepage: https://gatk.broadinstitute.org/hc/en-us - documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s - doi: 10.1158/1538-7445.AM2017-3590 - licence: ["Apache-2.0"] - identifier: "" +- gatk4: + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] + identifier: "" input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - bqsr_table: - type: file - description: Recalibration table from gatk4_baserecalibrator - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" +- - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - bqsr_table: + type: file + description: Recalibration table from gatk4_baserecalibrator + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) +- - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" +- - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" +- - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - bam: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.bam": - type: file - description: Recalibrated BAM file - pattern: "*.{bam}" - - cram: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.cram": - type: file - description: Recalibrated CRAM file - pattern: "*.{cram}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" +- bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{bam}" + - ${prefix}.bam: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{bam}" +- cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{cram}" + - ${prefix}.cram: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{cram}" +- versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@yocra3" - - "@FriederikeHanssen" - - "@maxulysse" +- "@yocra3" +- "@FriederikeHanssen" +- "@maxulysse" maintainers: - - "@yocra3" - - "@FriederikeHanssen" - - "@maxulysse" +- "@yocra3" +- "@FriederikeHanssen" +- "@maxulysse" 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 c4171be861..4af457d39f 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": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-02-15T10:12:13.226593047" + "timestamp": "2025-03-17T16:50:02.397152291" }, "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": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-02-15T11:43:27.971279286" + "timestamp": "2025-03-17T16:50:30.685886937" }, "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": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-02-15T11:40:33.915518205" + "timestamp": "2025-03-17T16:49:26.18719288" }, "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": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-02-15T11:42:52.310003463" + "timestamp": "2025-03-17T16:49:49.844595108" } } \ No newline at end of file From 3af46bc8a69bf8041e31c32a823ad4e01b60ca69 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Mon, 24 Mar 2025 12:44:08 -0400 Subject: [PATCH 03/11] Fix modules.json --- modules.json | 438 +++++++++++++-------------------------------------- 1 file changed, 109 insertions(+), 329 deletions(-) diff --git a/modules.json b/modules.json index 2fe818ef4f..66d7ee81ec 100644 --- a/modules.json +++ b/modules.json @@ -8,725 +8,517 @@ "ascat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/annotate": { "branch": "master", "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/mpileup": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "bam_ngscheckmate" - ] + "installed_by": ["bam_ngscheckmate"] }, "bcftools/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/stats": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/antitarget": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/batch": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/call": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/export": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/genemetrics": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/reference": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "controlfreec/assesssignificance": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff" }, "controlfreec/freec": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - 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"installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/mpileup": { "branch": "master", "git_sha": "13e7d1046922381df90cd8fe9bee8c3e57ae8457", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - 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"modules" - ] + "installed_by": ["modules"] }, "sentieon/gvcftyper": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/haplotyper": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/varcal": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff/download": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", "git_sha": "22f895866a1ad01556db175f9c0925ca90615d10", - "installed_by": [ - "modules", - "vcf_annotate_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "spring/decompress": { "branch": "master", "git_sha": "d7462e71f9129083ce10c3fe953ed401781e0ebd", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "strelka/germline": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "strelka/somatic": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": [ - "modules", - "vcf_annotate_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules", - "vcf_annotate_ensemblvep" - ] + "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "unzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcftools": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -735,47 +527,35 @@ "bam_ngscheckmate": { "branch": "master", "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_annotate_ensemblvep": { "branch": "master", "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_annotate_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 42cabd7b3ae98834106b957395678ab7484def5e Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Mon, 24 Mar 2025 13:36:01 -0400 Subject: [PATCH 04/11] updating gatk modules --- modules.json | 14 +- .../nf-core/gatk4/applybqsr/environment.yml | 6 +- modules/nf-core/gatk4/applybqsr/main.nf | 4 +- .../gatk4/applybqsr/tests/main.nf.test.snap | 56 +++--- .../gatk4/markduplicates/environment.yml | 6 +- modules/nf-core/gatk4/markduplicates/main.nf | 2 +- .../gatk4/mergemutectstats/environment.yml | 6 +- .../nf-core/gatk4/mergemutectstats/main.nf | 6 +- .../mergemutectstats/tests/main.nf.test.snap | 18 +- .../nf-core/gatk4/mergevcfs/environment.yml | 6 +- modules/nf-core/gatk4/mergevcfs/main.nf | 6 +- .../gatk4/mergevcfs/tests/main.nf.test | 3 + .../gatk4/mergevcfs/tests/main.nf.test.snap | 27 ++- modules/nf-core/gatk4/mutect2/environment.yml | 6 +- modules/nf-core/gatk4/mutect2/main.nf | 6 +- .../gatk4/mutect2/tests/main.nf.test.snap | 56 +++--- .../gatk4/variantrecalibrator/environment.yml | 6 +- .../nf-core/gatk4/variantrecalibrator/main.nf | 4 +- .../gatk4/variantrecalibrator/tests/AS.config | 7 + .../variantrecalibrator/tests/main.nf.test | 167 ++++++++++++++++++ .../tests/main.nf.test.snap | 133 ++++++++++++++ .../variantrecalibrator/tests/noAS.config | 8 + .../baserecalibrator/environment.yml | 4 +- .../gatk4spark/baserecalibrator/main.nf | 16 +- .../baserecalibrator/tests/main.nf.test | 160 +++++++++++++++++ .../baserecalibrator/tests/main.nf.test.snap | 167 ++++++++++++++++++ .../baserecalibrator/tests/nextflow.config | 2 + 27 files changed, 798 insertions(+), 104 deletions(-) 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 create mode 100644 modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config 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 diff --git a/modules.json b/modules.json index 66d7ee81ec..e4df8c09f0 100644 --- a/modules.json +++ b/modules.json @@ -181,7 +181,7 @@ }, "gatk4/applybqsr": { "branch": "master", - "git_sha": "6b3bf38285d94cc1ea3cd9fa93310d54b04c3819", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/applyvqsr": { @@ -267,27 +267,27 @@ }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/mergemutectstats": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/mutect2": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/variantrecalibrator": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4spark/applybqsr": { @@ -297,7 +297,7 @@ }, "gatk4spark/baserecalibrator": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4spark/markduplicates": { diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 4e91c311b0..5267454e8e 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYBQSR { conda "${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://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/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap index 19b37d0636..427cbddb8d 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/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 3c73c17e43..8afaba0656 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -1,8 +1,12 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 - bioconda::htslib=1.19.1 - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index baadefef41..cf770308d5 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -1,6 +1,6 @@ process GATK4_MARKDUPLICATES { tag "$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/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 06bce31e31..e6ddc6994c 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEMUTECTSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(stats) @@ -19,7 +19,7 @@ process GATK4_MERGEMUTECTSTATS { script: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${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/mergemutectstats/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap index d0279f272e..77da5d7820 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/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 9e8d43915c..1752f48a60 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -1,11 +1,11 @@ process GATK4_MERGEVCFS { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test index 77ace10a21..343fff68c9 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 62cceed57b..5fab6dca1b 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 diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 79d8d2826c..3ac374e035 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -1,11 +1,11 @@ process GATK4_MUTECT2 { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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/mutect2/tests/main.nf.test.snap b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap index f047af19dd..b37450f4f4 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/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 24844ce0c9..3c6048f4ba 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTRECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gatk4/variantrecalibrator/tests/AS.config b/modules/nf-core/gatk4/variantrecalibrator/tests/AS.config new file mode 100644 index 0000000000..eadb336e9d --- /dev/null +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/AS.config @@ -0,0 +1,7 @@ +process { + + publishDir = { "${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 0000000000..2ce4b46e53 --- /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.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.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.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', + '--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.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] + """ + } + } + + 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.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.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.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', + '--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.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] + """ + } + } + + 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.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.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.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', + '--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.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] + """ + } + } + + 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 0000000000..62882f25fa --- /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/modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config b/modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config new file mode 100644 index 0000000000..69efa09ea8 --- /dev/null +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config @@ -0,0 +1,8 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: GATK4_VARIANTRECALIBRATOR { + ext.args = '-mode SNP -an QD -an MQ -an FS -an SOR' + } +} diff --git a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml index 14075a574a..a5c49e9557 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4-spark=4.5.0.0 + - bioconda::gatk4-spark=4.6.1.0 diff --git a/modules/nf-core/gatk4spark/baserecalibrator/main.nf b/modules/nf-core/gatk4spark/baserecalibrator/main.nf index 32af761912..304b1bc524 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4spark/baserecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4SPARK_BASERECALIBRATOR { conda "${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 0000000000..ff6867d2f2 --- /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 0000000000..c02ce4b1c8 --- /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 0000000000..a1a17be887 --- /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' + From af50f23c8c9ee7c89b7f25eea8dadf526bec8598 Mon Sep 17 00:00:00 2001 From: John Orgera Date: Mon, 24 Mar 2025 13:36:54 -0400 Subject: [PATCH 05/11] updating gatk modules --- modules.json | 464 +++++++++++++----- .../nf-core/gatk4/applybqsr/environment.yml | 6 +- modules/nf-core/gatk4/applybqsr/main.nf | 4 +- .../gatk4/applybqsr/tests/main.nf.test.snap | 56 +-- .../gatk4/baserecalibrator/environment.yml | 6 +- .../nf-core/gatk4/baserecalibrator/main.nf | 14 +- .../nf-core/gatk4/baserecalibrator/meta.yml | 35 +- .../gatk4/baserecalibrator/tests/main.nf.test | 180 +++++-- .../baserecalibrator/tests/main.nf.test.snap | 155 ++++-- .../calculatecontamination/environment.yml | 6 +- .../gatk4/calculatecontamination/main.nf | 4 +- .../tests/main.nf.test.snap | 34 +- .../nf-core/gatk4/cnnscorevariants/README.md | 9 - .../gatk4/cnnscorevariants/environment.yml | 8 + .../nf-core/gatk4/cnnscorevariants/main.nf | 25 +- .../gatk4/cnnscorevariants/tests/main.nf.test | 77 +++ .../cnnscorevariants/tests/main.nf.test.snap | 65 +++ .../createsequencedictionary/environment.yml | 6 +- .../gatk4/createsequencedictionary/main.nf | 6 +- .../tests/main.nf.test.snap | 20 +- .../estimatelibrarycomplexity/environment.yml | 6 +- .../gatk4/estimatelibrarycomplexity/main.nf | 18 +- .../tests/main.nf.test | 2 +- .../tests/main.nf.test.snap | 26 +- .../gatk4/filtermutectcalls/environment.yml | 6 +- .../nf-core/gatk4/filtermutectcalls/main.nf | 4 +- .../filtermutectcalls/tests/main.nf.test.snap | 34 +- .../filtervarianttranches/environment.yml | 6 +- .../gatk4/filtervarianttranches/main.nf | 21 +- .../filtervarianttranches/tests/main.nf.test | 78 +++ .../tests/main.nf.test.snap | 65 +++ .../tests/nextflow.config | 6 + .../gatk4/gatherbqsrreports/environment.yml | 6 +- .../nf-core/gatk4/gatherbqsrreports/main.nf | 6 +- .../gatherbqsrreports/tests/main.nf.test.snap | 20 +- .../gatherpileupsummaries/environment.yml | 6 +- .../gatk4/gatherpileupsummaries/main.nf | 4 +- .../tests/main.nf.test.snap | 20 +- .../gatk4/genomicsdbimport/environment.yml | 6 +- .../nf-core/gatk4/genomicsdbimport/main.nf | 6 +- .../nf-core/gatk4/genomicsdbimport/meta.yml | 2 +- .../genomicsdbimport/tests/main.nf.test.snap | 34 +- .../gatk4/genotypegvcfs/environment.yml | 6 +- modules/nf-core/gatk4/genotypegvcfs/main.nf | 6 +- .../genotypegvcfs/tests/main.nf.test.snap | 50 +- .../gatk4/getpileupsummaries/environment.yml | 6 +- .../nf-core/gatk4/getpileupsummaries/main.nf | 4 +- .../tests/main.nf.test.snap | 38 +- .../gatk4/haplotypecaller/environment.yml | 6 +- modules/nf-core/gatk4/haplotypecaller/main.nf | 6 +- .../haplotypecaller/tests/main.nf.test.snap | 32 +- .../gatk4/intervallisttobed/environment.yml | 6 +- .../gatk4-intervallisttobed.diff | 6 +- .../nf-core/gatk4/intervallisttobed/main.nf | 16 +- .../intervallisttobed/tests/main.nf.test | 58 +++ .../intervallisttobed/tests/main.nf.test.snap | 72 +++ .../learnreadorientationmodel/environment.yml | 6 +- .../gatk4/learnreadorientationmodel/main.nf | 4 +- .../tests/main.nf.test.snap | 8 +- .../gatk4spark/markduplicates/environment.yml | 4 +- .../nf-core/gatk4spark/markduplicates/main.nf | 4 +- .../markduplicates/tests/main.nf.test.snap | 48 +- 62 files changed, 1453 insertions(+), 495 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 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 create mode 100644 modules/nf-core/gatk4/filtervarianttranches/tests/nextflow.config 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 diff --git a/modules.json b/modules.json index ad4fd57616..d9260faad8 100644 --- a/modules.json +++ b/modules.json @@ -8,507 +8,711 @@ "ascat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - 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"installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4spark/markduplicates": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", + "installed_by": [ + "modules" + ] }, "gawk": { "branch": "master", "git_sha": "97321eded31a12598837a476d3615300af413bb7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "goleft/indexcov": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "lofreq/callparallel": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "manta/germline": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "manta/somatic": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "manta/tumoronly": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mosdepth": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "msisensorpro/msisomatic": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "msisensorpro/scan": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ngscheckmate/ncm": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["bam_ngscheckmate"] + "installed_by": [ + "bam_ngscheckmate" + ] }, "samblaster": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/bam2fq": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/collatefastq": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/convert": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/mpileup": { "branch": "master", "git_sha": "13e7d1046922381df90cd8fe9bee8c3e57ae8457", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/view": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/applyvarcal": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/bwamem": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dedup": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnamodelapply": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnascope": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/gvcftyper": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/haplotyper": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/varcal": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "snpeff/download": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "snpeff/snpeff": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules", "vcf_annotate_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_snpeff" + ] }, "spring/decompress": { "branch": "master", "git_sha": "d7462e71f9129083ce10c3fe953ed401781e0ebd", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "strelka/germline": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "strelka/somatic": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/merge": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": ["modules", "vcf_annotate_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_snpeff" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules", "vcf_annotate_ensemblvep"] + "installed_by": [ + "modules", + "vcf_annotate_ensemblvep" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "unzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcftools": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -517,35 +721,47 @@ "bam_ngscheckmate": { "branch": "master", "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_ensemblvep": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 4e91c311b0..5267454e8e 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYBQSR { conda "${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://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/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap index 19b37d0636..427cbddb8d 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/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 1a29986265..493533c726 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -4,16 +4,16 @@ process GATK4_BASERECALIBRATOR { conda "${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://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 fasta - path fai - path dict - path known_sites - path known_sites_tbi + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(known_sites) + tuple val(meta6), path(known_sites_tbi) output: tuple val(meta), path("*.table"), emit: table diff --git a/modules/nf-core/gatk4/baserecalibrator/meta.yml b/modules/nf-core/gatk4/baserecalibrator/meta.yml index 876b796039..c3caeb8084 100644 --- a/modules/nf-core/gatk4/baserecalibrator/meta.yml +++ b/modules/nf-core/gatk4/baserecalibrator/meta.yml @@ -34,23 +34,48 @@ input: - intervals: type: file description: Bed file with the genomic regions included in the library (optional) - - - fasta: + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fasta: type: file description: The reference fasta file pattern: "*.fasta" - - - fai: + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fai: type: file description: Index of reference fasta file pattern: "*.fasta.fai" - - - dict: + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - dict: type: file description: GATK sequence dictionary pattern: "*.dict" - - - known_sites: + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - known_sites: type: file description: VCF files with known sites for indels / snps (optional) pattern: "*.vcf.gz" - - - known_sites_tbi: + - - meta6: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - known_sites_tbi: type: file description: Tabix index of the known_sites (optional) pattern: "*.vcf.gz.tbi" diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test index fbd91beae2..97c1c1ecb1 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test @@ -13,18 +13,17 @@ nextflow_process { when { process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) - input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) - + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) """ } } @@ -35,26 +34,23 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - bam - intervals") { when { process { """ - - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) - input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) - + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) """ } } @@ -72,25 +68,23 @@ nextflow_process { when { process { """ - - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) - input[4] = [ + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - ] - input[5] = [ + ]) + input[5] = Channel.of([ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - ] - + ]) """ } } @@ -101,7 +95,34 @@ nextflow_process { { assert snapshot(process.out).match() } ) } + } + + test("homo_sapiens - cram") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + [] + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)]) + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } } test("sarscov2 - bam - stub") { @@ -110,17 +131,46 @@ nextflow_process { when { process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map - [], - [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] - ] - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 - bam - intervals - stub") { + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) """ } } @@ -134,22 +184,58 @@ nextflow_process { } - test("homo_sapiens - cram ") { + test("sarscov2 - bam - multiple sites - stub") { + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ]) + input[5] = Channel.of([ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - cram - stub") { + options "-stub" when { process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', 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) - input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)]) """ } } @@ -160,7 +246,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } 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 8291304ba8..efdf46b3df 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap @@ -1,4 +1,37 @@ { + "homo_sapiens - cram": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + ] + ], + "1": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + ] + ], + "versions": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-23T15:37:29.36262858" + }, "sarscov2 - bam - stub": { "content": [ { @@ -11,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -22,15 +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": "2024-02-13T16:16:00.04396" + "timestamp": "2024-10-31T10:36:20.634357503" }, "sarscov2 - bam - intervals": { "content": [ @@ -44,7 +77,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -55,15 +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": "2024-02-13T16:15:17.899391" + "timestamp": "2024-10-31T10:35:55.223087741" }, "sarscov2 - bam - multiple sites": { "content": [ @@ -77,7 +110,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -88,17 +121,17 @@ ] ], "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 ": { + "homo_sapiens - cram - stub": { "content": [ { "0": [ @@ -106,30 +139,30 @@ { "id": "test" }, - "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ { "id": "test" }, - "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-02-13T16:16:42.135898" + "timestamp": "2025-01-23T15:38:23.045092592" }, "sarscov2 - bam": { "content": [ @@ -143,7 +176,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -154,14 +187,80 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T10:35:41.89476551" + }, + "sarscov2 - bam - intervals - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-23T15:37:56.722728282" + }, + "sarscov2 - bam - multiple sites - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-02-13T16:14:57.629443" + "timestamp": "2025-01-23T15:38:09.797767675" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 1ca3fd9d45..20fe3c5e13 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -4,8 +4,8 @@ process GATK4_CALCULATECONTAMINATION { conda "${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://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/calculatecontamination/tests/main.nf.test.snap b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap index 5c2930f948..756c2452f8 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/cnnscorevariants/README.md b/modules/nf-core/gatk4/cnnscorevariants/README.md deleted file mode 100644 index c6a4545655..0000000000 --- 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 0000000000..da693d88d5 --- /dev/null +++ b/modules/nf-core/gatk4/cnnscorevariants/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf index 92de2267e0..5ff13b41d1 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -28,10 +28,10 @@ process GATK4_CNNSCOREVARIANTS { } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${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 . \\ $args @@ -59,4 +59,17 @@ process GATK4_CNNSCOREVARIANTS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo "" | gzip -c > ${prefix}.cnn.vcf.gz + touch ${prefix}.cnn.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${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 0000000000..db58bf421c --- /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.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.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, [], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + path(process.out.vcf[0][1]).vcf.variantsMD5, + 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.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.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, [], []] + """ + } + } + + 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 0000000000..63be00cfee --- /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" + ], + "34e15624519ba7408d53cb8bb365ffc1", + "test.cnn.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-18T09:39:27.896072791" + }, + "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/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index c7f1d75b3c..998622a065 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -1,11 +1,11 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap index 16735f9549..e8a600fd11 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/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index e0744e16f7..9071279577 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -1,11 +1,11 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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) @@ -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 e23b65573c..8552ca47dc 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 bbcef1471e..73752535e9 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap @@ -3,39 +3,39 @@ "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": { + "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": [ "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/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 0532ec0258..d3c5bb5ad7 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERMUTECTCALLS { conda "${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://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/filtermutectcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap index 1c39e3b5d7..28a63357e7 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/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 05489e179b..c5249b7a05 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERVARIANTTRANCHES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(intervals) @@ -27,7 +27,7 @@ process GATK4_FILTERVARIANTTRANCHES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${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 0000000000..c315ed8fc0 --- /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.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.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) + """ + } + } + + 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.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.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) + """ + } + } + + 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 0000000000..8bc251b61c --- /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/modules/nf-core/gatk4/filtervarianttranches/tests/nextflow.config b/modules/nf-core/gatk4/filtervarianttranches/tests/nextflow.config new file mode 100644 index 0000000000..7a8f0a061b --- /dev/null +++ b/modules/nf-core/gatk4/filtervarianttranches/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + ext.args = "--info-key CNN_1D" +} diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 79667a2994..fdc5a2a723 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -1,11 +1,11 @@ process GATK4_GATHERBQSRREPORTS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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/gatherbqsrreports/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap index bc5d4bd133..e792d07ec5 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/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index bcafd544b4..af397a1a2d 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GATHERPILEUPSUMMARIES { conda "${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://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/gatherpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap index fd9f258344..e7094d73f4 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/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 6f1d4c5370..90f1200dc7 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -1,11 +1,11 @@ process GATK4_GENOMICSDBIMPORT { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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/genomicsdbimport/meta.yml b/modules/nf-core/gatk4/genomicsdbimport/meta.yml index 174ae2eb0a..ba734b288f 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/meta.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/meta.yml @@ -38,7 +38,7 @@ input: pattern: "*.interval_list" - interval_value: type: string - description: if an intervals file has not been spcified, the value enetered + description: if an intervals file has not been specified, the value entered here will be used as an interval via the "-L" argument pattern: "example: chr1:1000-10000" - wspace: 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 55ced0d880..cb47a432c9 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/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index f180f74975..dc2813a350 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -1,11 +1,11 @@ process GATK4_GENOTYPEGVCFS { tag "$meta.id" - label 'process_high' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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/genotypegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap index 1621618e7a..30e2dc1cc6 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/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 43611271e0..41fd312811 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GETPILEUPSUMMARIES { conda "${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://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/getpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap index d9304bcdc5..e44c13bad8 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/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index b2aff48969..1ef76789de 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -1,11 +1,11 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap index 0203fcfcf4..e3ba2bdfa9 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/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff b/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff index 03086949c6..8f61ed1b3d 100644 --- a/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff +++ b/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff @@ -1,10 +1,10 @@ -Changes in module 'nf-core/gatk4/intervallisttobed' +Changes in component 'nf-core/gatk4/intervallisttobed' 'modules/nf-core/gatk4/intervallisttobed/environment.yml' is unchanged 'modules/nf-core/gatk4/intervallisttobed/meta.yml' is unchanged Changes in 'gatk4/intervallisttobed/main.nf': --- modules/nf-core/gatk4/intervallisttobed/main.nf +++ modules/nf-core/gatk4/intervallisttobed/main.nf -@@ -40,4 +40,18 @@ +@@ -52,4 +52,18 @@ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ @@ -24,4 +24,6 @@ Changes in 'gatk4/intervallisttobed/main.nf': + """ } +'modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test' is unchanged +'modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test.snap' is unchanged ************************************************************ diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 743bb3413a..3d8a4689dc 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOBED { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) @@ -41,6 +41,18 @@ process GATK4_INTERVALLISTTOBED { END_VERSIONS """ + stub: + def prefix = task.ext.prefix ?: "${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 + """ + stub: def prefix = task.ext.prefix ?: "${meta.id}.cram" def metrics = task.ext.metrics ?: "${prefix}.metrics" 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 0000000000..33bf46fbf1 --- /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.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.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.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.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 0000000000..0664f5e913 --- /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/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index 55993f440c..b562b72c74 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index a61b292812..86e7daaa6c 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_LEARNREADORIENTATIONMODEL { conda "${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://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/learnreadorientationmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap index b829bd9c4a..638e058359 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/gatk4spark/markduplicates/environment.yml b/modules/nf-core/gatk4spark/markduplicates/environment.yml index 14075a574a..a5c49e9557 100644 --- a/modules/nf-core/gatk4spark/markduplicates/environment.yml +++ b/modules/nf-core/gatk4spark/markduplicates/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4-spark=4.5.0.0 + - bioconda::gatk4-spark=4.6.1.0 diff --git a/modules/nf-core/gatk4spark/markduplicates/main.nf b/modules/nf-core/gatk4spark/markduplicates/main.nf index b6a6daffea..9cb74c8b36 100644 --- a/modules/nf-core/gatk4spark/markduplicates/main.nf +++ b/modules/nf-core/gatk4spark/markduplicates/main.nf @@ -4,8 +4,8 @@ process GATK4SPARK_MARKDUPLICATES { conda "${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 4968a1ce65..f9366caead 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 From 826a7aefbd601c860744720e197c0bc3b133d157 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Mon, 24 Mar 2025 14:09:48 -0400 Subject: [PATCH 06/11] Update CHANGELOG.md --- CHANGELOG.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 78f05380cb..58bb10f18c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,8 +5,6 @@ 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). -<<<<<<< HEAD -======= ## dev ### Added @@ -43,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1806](https://github.com/nf-core/sarek/pull/1806) - Use `nft-vcf` for nf-test vcf assertions - [1814](https://github.com/nf-core/sarek/pull/1814) - Added link to Bluesky - [1829](https://github.com/nf-core/sarek/pull/1829) - Add muse as variant caller to images +- [1835](https://github.com/nf-core/sarek/pull/1835) - Add GPU testing possibilities #### Changed @@ -72,7 +71,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1814](https://github.com/nf-core/sarek/pull/1814) - Removed link to Twitter/X ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e ## [3.5.1](https://github.com/nf-core/sarek/releases/tag/3.5.1) - Akkatjåkkå Akkatjåkkå is another glacier. From 1b64724d0e7a50ad5b33876298640562b1334673 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Mon, 24 Mar 2025 14:11:34 -0400 Subject: [PATCH 07/11] Update multiqc_config.yml --- assets/multiqc_config.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e9c4e00313..67362dcfeb 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,15 +3,10 @@ custom_logo_url: https://github.com/nf-core/sarek/ custom_logo_title: "nf-core/sarek" report_comment: > -<<<<<<< HEAD - This report has been generated by the nf-core/sarek analysis pipeline. For information about how to - interpret these results, please see the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the >>>>>> 42cabd7b3ae98834106b957395678ab7484def5e target="_blank">documentation. report_section_order: "nf-core-sarek-methods-description": From 0b4e79819a2ba75cc87e69e3bd1a3293cc12b5f9 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Mon, 24 Mar 2025 14:20:07 -0400 Subject: [PATCH 08/11] merge markers removed --- tests/annotation_merge.nf.test.snap | 8 -------- tests/annotation_snpeff.nf.test.snap | 4 ---- tests/annotation_vep.nf.test.snap | 4 ---- tests/default.nf.test.snap | 4 ---- tests/save_output_as_bam.nf.test.snap | 4 ---- tests/saved_mapped.nf.test.snap | 4 ---- tests/sentieon.nf.test.snap | 4 ---- tests/tumor-normal-pair.nf.test.snap | 4 ---- 8 files changed, 36 deletions(-) diff --git a/tests/annotation_merge.nf.test.snap b/tests/annotation_merge.nf.test.snap index 8ec0c184f6..f0a7bfa686 100644 --- a/tests/annotation_merge.nf.test.snap +++ b/tests/annotation_merge.nf.test.snap @@ -17,11 +17,7 @@ "tabix": 1.2 }, "Workflow": { -<<<<<<< HEAD - "nf-core/sarek": "v3.5.1" -======= "nf-core/sarek": "v3.6.0dev" ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e } }, [ @@ -142,11 +138,7 @@ "tabix": 1.2 }, "Workflow": { -<<<<<<< HEAD - "nf-core/sarek": "v3.5.1" -======= "nf-core/sarek": "v3.6.0dev" ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e } }, [ diff --git a/tests/annotation_snpeff.nf.test.snap b/tests/annotation_snpeff.nf.test.snap index 702ac08855..10e5382ed1 100644 --- a/tests/annotation_snpeff.nf.test.snap +++ b/tests/annotation_snpeff.nf.test.snap @@ -10,11 +10,7 @@ "tabix": 1.2 }, "Workflow": { -<<<<<<< HEAD - "nf-core/sarek": "v3.5.1" -======= "nf-core/sarek": "v3.6.0dev" ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e } }, [ diff --git a/tests/annotation_vep.nf.test.snap b/tests/annotation_vep.nf.test.snap index 3971d8896e..44fb0825ae 100644 --- a/tests/annotation_vep.nf.test.snap +++ b/tests/annotation_vep.nf.test.snap @@ -11,11 +11,7 @@ "tabix": 1.2 }, "Workflow": { -<<<<<<< HEAD - "nf-core/sarek": "v3.5.1" -======= "nf-core/sarek": "v3.6.0dev" ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e } }, [ diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 44b70608b6..f1effac055 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -39,11 +39,7 @@ "vcftools": "0.1.16" }, "Workflow": { -<<<<<<< HEAD - "nf-core/sarek": "v3.5.1" -======= "nf-core/sarek": "v3.6.0dev" ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e } }, [ diff --git a/tests/save_output_as_bam.nf.test.snap b/tests/save_output_as_bam.nf.test.snap index ca3d9771e7..f762b4bbed 100644 --- a/tests/save_output_as_bam.nf.test.snap +++ b/tests/save_output_as_bam.nf.test.snap @@ -17,11 +17,7 @@ "samtools": 1.21 }, "Workflow": { -<<<<<<< HEAD - "nf-core/sarek": "v3.5.1" -======= "nf-core/sarek": "v3.6.0dev" ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e } }, [ diff --git a/tests/saved_mapped.nf.test.snap b/tests/saved_mapped.nf.test.snap index 2906db178b..b309c97103 100644 --- a/tests/saved_mapped.nf.test.snap +++ b/tests/saved_mapped.nf.test.snap @@ -17,11 +17,7 @@ "samtools": 1.21 }, "Workflow": { -<<<<<<< HEAD - "nf-core/sarek": "v3.5.1" -======= "nf-core/sarek": "v3.6.0dev" ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e } }, [ diff --git a/tests/sentieon.nf.test.snap b/tests/sentieon.nf.test.snap index 115203d7d2..b8ec1d981c 100644 --- a/tests/sentieon.nf.test.snap +++ b/tests/sentieon.nf.test.snap @@ -39,11 +39,7 @@ "vcftools": "0.1.16" }, "Workflow": { -<<<<<<< HEAD - "nf-core/sarek": "v3.5.1" -======= "nf-core/sarek": "v3.6.0dev" ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e } }, [ diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap index 5c4f50f597..bac70d0020 100644 --- a/tests/tumor-normal-pair.nf.test.snap +++ b/tests/tumor-normal-pair.nf.test.snap @@ -42,11 +42,7 @@ "vcftools": "0.1.16" }, "Workflow": { -<<<<<<< HEAD - "nf-core/sarek": "v3.5.1" -======= "nf-core/sarek": "v3.6.0dev" ->>>>>>> 42cabd7b3ae98834106b957395678ab7484def5e } }, [ From b54919a7c34a05bfc8c97e7383eaadf0ec643d1f Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Mon, 24 Mar 2025 14:28:54 -0400 Subject: [PATCH 09/11] Update modules.json --- modules.json | 371 +++++++++++++-------------------------------------- 1 file changed, 93 insertions(+), 278 deletions(-) diff --git a/modules.json b/modules.json index ba6dfe4c11..330993c19f 100644 --- a/modules.json +++ b/modules.json @@ -8,187 +8,135 @@ "ascat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/annotate": { "branch": "master", "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/mpileup": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "bam_ngscheckmate" - ] + "installed_by": ["bam_ngscheckmate"] }, "bcftools/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/stats": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/antitarget": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/batch": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/call": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/export": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/genemetrics": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvkit/reference": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "controlfreec/assesssignificance": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff" }, "controlfreec/freec": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "controlfreec/freec2bed": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "controlfreec/freec2circos": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "controlfreec/makegraph2": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "dragmap/align": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/dragmap/align/dragmap-align.diff" }, "dragmap/hashtable": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff" }, "ensemblvep/download": { @@ -204,44 +152,32 @@ "fastp": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fgbio/callmolecularconsensusreads": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fgbio/fastqtobam": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fgbio/groupreadsbyumi": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "freebayes": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/applybqsr": { "branch": "master", @@ -251,115 +187,83 @@ "gatk4/applyvqsr": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/baserecalibrator": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/calculatecontamination": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/cnnscorevariants": { "branch": "master", "git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/estimatelibrarycomplexity": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/filtermutectcalls": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/filtervarianttranches": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/gatherbqsrreports": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/gatherpileupsummaries": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/genomicsdbimport": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/genotypegvcfs": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/getpileupsummaries": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/intervallisttobed": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff" }, "gatk4/learnreadorientationmodel": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/markduplicates": { "branch": "master", @@ -399,79 +303,57 @@ "gatk4spark/markduplicates": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gawk": { "branch": "master", "git_sha": "97321eded31a12598837a476d3615300af413bb7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "goleft/indexcov": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "lofreq/callparallel": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "manta/germline": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "manta/somatic": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "manta/tumoronly": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "msisensorpro/msisomatic": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "msisensorpro/scan": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "muse/call": { "branch": "master", @@ -486,135 +368,97 @@ "ngscheckmate/ncm": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "bam_ngscheckmate" - ] + "installed_by": ["bam_ngscheckmate"] }, "samblaster": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/bam2fq": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/collatefastq": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/mpileup": { "branch": "master", "git_sha": "13e7d1046922381df90cd8fe9bee8c3e57ae8457", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/view": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/applyvarcal": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/bwamem": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dedup": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dnamodelapply": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dnascope": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/gvcftyper": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/haplotyper": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/varcal": { "branch": "master", "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff/download": { "branch": "master", @@ -629,38 +473,27 @@ "spring/decompress": { "branch": "master", "git_sha": "d7462e71f9129083ce10c3fe953ed401781e0ebd", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "strelka/germline": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "strelka/somatic": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": [ - "modules", - "vcf_annotate_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { "branch": "master", @@ -670,30 +503,22 @@ "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "unzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcftools": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -702,30 +527,22 @@ "bam_ngscheckmate": { "branch": "master", "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_annotate_ensemblvep": { "branch": "master", @@ -735,12 +552,10 @@ "vcf_annotate_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 7ffb226157f786ebd476107b693ba73bdb681fce Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Mon, 24 Mar 2025 14:49:02 -0400 Subject: [PATCH 10/11] Update main.nf --- modules/nf-core/gatk4/intervallisttobed/main.nf | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 3d8a4689dc..ae68cb28e5 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -52,18 +52,4 @@ process GATK4_INTERVALLISTTOBED { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}.cram" - def metrics = task.ext.metrics ?: "${prefix}.metrics" - def prefix_basename = prefix.substring(0, prefix.lastIndexOf(".")) - - """ - touch ${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') - END_VERSIONS - """ -} +} \ No newline at end of file From 48d13d55c221855cf5f147a5ff01014f0b43fc2c Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Mon, 24 Mar 2025 15:25:19 -0400 Subject: [PATCH 11/11] base recalibrator --- subworkflows/local/bam_baserecalibrator/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/bam_baserecalibrator/main.nf b/subworkflows/local/bam_baserecalibrator/main.nf index 285ad6b856..5afce175be 100644 --- a/subworkflows/local/bam_baserecalibrator/main.nf +++ b/subworkflows/local/bam_baserecalibrator/main.nf @@ -26,7 +26,7 @@ workflow BAM_BASERECALIBRATOR { .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ] } // RUN BASERECALIBRATOR - GATK4_BASERECALIBRATOR(cram_intervals, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] }, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi) + GATK4_BASERECALIBRATOR(cram_intervals, fasta.map{ meta, it -> [ meta, it ] }, fasta_fai.map{ meta, it -> [ meta, it ] }, dict.map{ meta, it -> [ meta, it ] }, known_sites, known_sites_tbi) // Figuring out if there is one or more table(s) from the same sample table_to_merge = GATK4_BASERECALIBRATOR.out.table.map{ meta, table -> [ groupKey(meta, meta.num_intervals), table ] }.groupTuple().branch{