diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 9bc6f98a..8309f86c 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,4 +1,3 @@ - # Description @@ -6,22 +5,21 @@ ### Closes #... ## Testing Results - -- Tumor/Normal Paired Sample: + +- Case 1 - sample: - - input YAML: + - input csv: - config: - output: -- Tumor-only Sample: +- Case 2 - sample: - - input YAML: + - input csv: - config: - output: -- Multi-tumor Sample: - - sample: - - input YAML: - - config: +- NFTest - output: + - log: + - cases: # Checklist @@ -34,7 +32,7 @@ - [ ] I have set up or verified the branch protection rule following the [github standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190380/GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request. -- [ ] I have added my name to the contributors listings in the ``manifest`` block in the `nextflow.config` as part of this pull request; I am listed already, or do not wish to be listed. (*This acknowledgement is optional.*) +- [ ] I have added my name to the contributors listings in the ``manifest`` block in the `nextflow.config` as part of this pull request, am listed already, or do not wish to be listed. (*This acknowledgement is optional.*) - [ ] I have added the changes included in this pull request to the `CHANGELOG.md` under the next release version or unreleased, and updated the date. diff --git a/CHANGELOG.md b/CHANGELOG.md index d6648204..9e162442 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,14 @@ 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). ## [Unreleased] +### Changed +- Update PipeVal 4.0.0-rc.2 -> 5.1.0 +- Update GATK 4.5.0.0 -> 4.6.1.0 +- Update bam_readcount 0.8.0 -> 1.0.1 +- Update MuSE 2.0.4 -> MuSE 2.1.2 +- Update BCFtools 1.17 -> 1.21 +- Update NFtest for new tool versions + ### Added - Use `methods.setup_process_afterscript()` for process logs - Output pipeline parameters to log directory using `store_object_as_json` diff --git a/config/default.config b/config/default.config index fd50f3fc..5cf372aa 100644 --- a/config/default.config +++ b/config/default.config @@ -18,15 +18,15 @@ params { docker_container_registry = "ghcr.io/uclahs-cds" //algorithm version - pipeval_version = "4.0.0-rc.2" - GATK_version = "4.5.0.0" + pipeval_version = "5.1.0" + GATK_version = "4.6.1.0" somaticsniper_version = "1.0.5.0" - bam_readcount_version = "0.8.0" + bam_readcount_version = "1.0.1" ubuntu_version = "20.04" strelka2_version = "2.9.10" manta_version = "1.6.0" - MuSE_version = "2.0.4" - BCFtools_version = "1.17" + MuSE_version = "2.1.2" + BCFtools_version = "1.21" call_ssnv_r_version = "dev" vcf2maf_version = "v1.6.18" bpg_version = "7.1.0" @@ -34,7 +34,7 @@ params { docker_image_validate_params = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}" docker_image_GATK = "broadinstitute/gatk:${params.GATK_version}" docker_image_somaticsniper = "${-> params.docker_container_registry}/somaticsniper:${params.somaticsniper_version}" - docker_image_bam_readcount = "${-> params.docker_container_registry}/bam-readcount:${params.bam_readcount_version}" + docker_image_bam_readcount = "${-> params.docker_container_registry}/bam_readcount:${params.bam_readcount_version}" docker_image_ubuntu = "ubuntu:${params.ubuntu_version}" docker_image_strelka2 = "${-> params.docker_container_registry}/strelka2:${params.strelka2_version}" docker_image_manta = "${-> params.docker_container_registry}/manta:${params.manta_version}" diff --git a/metadata.yaml b/metadata.yaml index 3f90afb6..d08c95cd 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -5,4 +5,4 @@ Maintainers: [sfitzgibbon@mednet.ucla.edu] Contributors: ['Mao Tian', 'Bugh Caden', 'Helena Winata', 'Yash Patel', 'Sorel Fitz-Gibbon'] Languages: ['Docker', 'Nextflow'] Dependencies: ['Docker', 'Nextflow'] -Tools: ['GATK 4.5.0.0', 'SomaticSniper v1.0.5.0', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0.4', 'BCFtools v1.17', 'R v4.3.1', 'VennDiagram v1.7.3', 'vcf2maf v1.6.18'] +Tools: ['GATK 4.6.1.0', 'SomaticSniper v1.0.5.0', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.1.2', 'BCFtools v1.21', 'R v4.3.1', 'VennDiagram v1.7.3', 'vcf2maf v1.6.18'] diff --git a/nftest.yml b/nftest.yml index 6cbc8f30..c7b31948 100644 --- a/nftest.yml +++ b/nftest.yml @@ -15,71 +15,71 @@ cases: verbose: true asserts: - actual: call-sSNV-*/S2-v1.1.5/MuSE-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/MuSE-2.0.3/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/MuSE-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/MuSE-2.0.3/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/SomaticSniper-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2 - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2 + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2 method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-1-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-2-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Intersect-BCFtools-1.17/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Intersect-BCFtools-1.17/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Intersect-BCFtools-1.17/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/S2-v1.1.5/Intersect-BCFtools-1.17/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh - name: a_mini-mutect2-tumor-only @@ -91,15 +91,15 @@ cases: verbose: true asserts: - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/S2-v1.1.5/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/S2-v1.1.5/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/S2-v1.1.5/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - name: a_mini-mutect2-multiple-samples @@ -111,15 +111,15 @@ cases: verbose: true asserts: - actual: call-sSNV-*/TWGSAMIN000001/Mutect2-*/output/Mutect2-*_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/TWGSAMIN000001/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.4.0_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/TWGSAMIN000001/Mutect2-*/output/Mutect2-*_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/TWGSAMIN000001/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/TWGSAMIN000001/Mutect2-*/output/Mutect2-*_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/TWGSAMIN000001/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz script: test/assert_vcf.sh - name: a_mini-two-tools @@ -131,43 +131,43 @@ cases: verbose: true asserts: - actual: call-sSNV-*/S2-v1.1.5/SomaticSniper-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2 - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2 + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2 method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-1-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-2-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/Intersect-BCFtools-1.17/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/S2-v1.1.5/Intersect-BCFtools-1.17/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh - name: a_mini-somaticsniper @@ -179,7 +179,7 @@ cases: verbose: true asserts: - actual: call-sSNV-*/S2-v1.1.5/SomaticSniper-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-somaticsniper/S2-v1.1.5/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - name: a_mini-strelka2 @@ -191,11 +191,11 @@ cases: verbose: true asserts: - actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-strelka2/S2-v1.1.5/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-strelka2/S2-v1.1.5/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - name: a_mini-mutect2 @@ -207,15 +207,15 @@ cases: verbose: true asserts: - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2/S2-v1.1.5/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2/S2-v1.1.5/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2/S2-v1.1.5/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - name: a_mini-muse @@ -227,7 +227,7 @@ cases: verbose: true asserts: - actual: call-sSNV-*/S2-v1.1.5/MuSE-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-muse/S2-v1.1.5/MuSE-2.0.3/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz script: test/assert_vcf.sh - name: a_mini-all-tools-vcf-input @@ -239,37 +239,37 @@ cases: verbose: true asserts: - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-vcf-input/S2-v1.1.5/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2 - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-vcf-input/S2-v1.1.5/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2 + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2 method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-vcf-input/S2-v1.1.5/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-1-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-vcf-input/S2-v1.1.5/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-2-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-vcf-input/S2-v1.1.5/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt method: md5 - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-vcf-input/S2-v1.1.5/Intersect-BCFtools-1.17/MuSE-2.0.4_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-vcf-input/S2-v1.1.5/Intersect-BCFtools-1.17/Mutect2-4.5.0.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-vcf-input/S2-v1.1.5/Intersect-BCFtools-1.17/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-vcf-input/S2-v1.1.5/Intersect-BCFtools-1.17/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz script: test/assert_vcf.sh diff --git a/test/configtest-F16.json b/test/configtest-F16.json index 1ccf0594..ecd72719 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -54,16 +54,16 @@ "version": "VER.SI.ON" }, "params": { - "BCFtools_version": "1.17", - "GATK_version": "4.5.0.0", - "MuSE_version": "2.0.4", + "BCFtools_version": "1.21", + "GATK_version": "4.6.1.0", + "MuSE_version": "2.1.2", "algorithm": [ "somaticsniper", "strelka2", "mutect2", "muse" ], - "bam_readcount_version": "0.8.0", + "bam_readcount_version": "1.0.1", "bgzip_extra_args": "", "bpg_version": "7.1.0", "cache_intermediate_pipeline_steps": false, @@ -71,10 +71,10 @@ "dataset_id": "TWGSAMIN", "dbSNP": "/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz", "docker_container_registry": "ghcr.io/uclahs-cds", - "docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.17", - "docker_image_GATK": "broadinstitute/gatk:4.5.0.0", - "docker_image_MuSE": "ghcr.io/uclahs-cds/muse:2.0.4", - "docker_image_bam_readcount": "ghcr.io/uclahs-cds/bam-readcount:0.8.0", + "docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.21", + "docker_image_GATK": "broadinstitute/gatk:4.6.1.0", + "docker_image_MuSE": "ghcr.io/uclahs-cds/muse:2.1.2", + "docker_image_bam_readcount": "ghcr.io/uclahs-cds/bam_readcount:1.0.1", "docker_image_bpg": "ghcr.io/uclahs-cds/boutroslabplottinggeneral:7.1.0", "docker_image_manta": "ghcr.io/uclahs-cds/manta:1.6.0", "docker_image_r_VennDiagram": "ghcr.io/uclahs-cds/call-ssnv-r:dev", @@ -82,7 +82,7 @@ "docker_image_src_util": "ghcr.io/uclahs-cds/src-util:1.2.0", "docker_image_strelka2": "ghcr.io/uclahs-cds/strelka2:2.9.10", "docker_image_ubuntu": "ubuntu:20.04", - "docker_image_validate_params": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2", + "docker_image_validate_params": "ghcr.io/uclahs-cds/pipeval:5.1.0", "docker_image_vcf2maf": "ghcr.io/mskcc/vcf2maf/vcf2maf:v1.6.18", "exome": false, "filter_mutect_calls_extra_args": "", @@ -120,7 +120,7 @@ "output_dir_base": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847", "panel_of_normals_vcf": "", "patient_id": "TWGSAMIN000001", - "pipeval_version": "4.0.0-rc.2", + "pipeval_version": "5.1.0", "proc_resource_params": { "call_sIndel_Manta": { "cpus": "6", diff --git a/test/configtest-F32.json b/test/configtest-F32.json index 1b0f883f..c9319c57 100644 --- a/test/configtest-F32.json +++ b/test/configtest-F32.json @@ -54,16 +54,16 @@ "version": "VER.SI.ON" }, "params": { - "BCFtools_version": "1.17", - "GATK_version": "4.5.0.0", - "MuSE_version": "2.0.4", + "BCFtools_version": "1.21", + "GATK_version": "4.6.1.0", + "MuSE_version": "2.1.2", "algorithm": [ "somaticsniper", "strelka2", "mutect2", "muse" ], - "bam_readcount_version": "0.8.0", + "bam_readcount_version": "1.0.1", "bgzip_extra_args": "", "bpg_version": "7.1.0", "cache_intermediate_pipeline_steps": false, @@ -71,10 +71,10 @@ "dataset_id": "TWGSAMIN", "dbSNP": "/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz", "docker_container_registry": "ghcr.io/uclahs-cds", - "docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.17", - "docker_image_GATK": "broadinstitute/gatk:4.5.0.0", - "docker_image_MuSE": "ghcr.io/uclahs-cds/muse:2.0.4", - "docker_image_bam_readcount": "ghcr.io/uclahs-cds/bam-readcount:0.8.0", + "docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.21", + "docker_image_GATK": "broadinstitute/gatk:4.6.1.0", + "docker_image_MuSE": "ghcr.io/uclahs-cds/muse:2.1.2", + "docker_image_bam_readcount": "ghcr.io/uclahs-cds/bam_readcount:1.0.1", "docker_image_bpg": "ghcr.io/uclahs-cds/boutroslabplottinggeneral:7.1.0", "docker_image_manta": "ghcr.io/uclahs-cds/manta:1.6.0", "docker_image_r_VennDiagram": "ghcr.io/uclahs-cds/call-ssnv-r:dev", @@ -82,7 +82,7 @@ "docker_image_src_util": "ghcr.io/uclahs-cds/src-util:1.2.0", "docker_image_strelka2": "ghcr.io/uclahs-cds/strelka2:2.9.10", "docker_image_ubuntu": "ubuntu:20.04", - "docker_image_validate_params": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2", + "docker_image_validate_params": "ghcr.io/uclahs-cds/pipeval:5.1.0", "docker_image_vcf2maf": "ghcr.io/mskcc/vcf2maf/vcf2maf:v1.6.18", "exome": false, "filter_mutect_calls_extra_args": "", @@ -120,7 +120,7 @@ "output_dir_base": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847", "panel_of_normals_vcf": "", "patient_id": "TWGSAMIN000001", - "pipeval_version": "4.0.0-rc.2", + "pipeval_version": "5.1.0", "proc_resource_params": { "call_sIndel_Manta": { "cpus": "8",