From 9990edc385cbd9fc49121908a52bc2efee9f19e9 Mon Sep 17 00:00:00 2001 From: Yash Patel Date: Wed, 18 Oct 2023 10:14:17 -0700 Subject: [PATCH 1/3] Switch to native bzip2 from ubuntu image --- config/default.config | 4 ++-- module/common.nf | 13 ++++++------- module/intersect.nf | 10 +++++----- module/somaticsniper.nf | 8 ++++---- 4 files changed, 17 insertions(+), 18 deletions(-) diff --git a/config/default.config b/config/default.config index 8da211f6..8ed710c0 100644 --- a/config/default.config +++ b/config/default.config @@ -19,7 +19,7 @@ params { GATK_version = "4.4.0.0" somaticsniper_version = "1.0.5.0" bam_readcount_version = "0.8.0" - blarchive_version = "2.0.0" + ubuntu_version = "23.04" strelka2_version = "2.9.10" manta_version = "1.6.0" MuSE_version = "2.0.3" @@ -31,7 +31,7 @@ params { 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:${params.bam_readcount_version}" - docker_image_blarchive = "${-> params.docker_container_registry}/blarchive:${params.blarchive_version}" + docker_image_ubuntu = "ubuntu:${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}" docker_image_MuSE = "${-> params.docker_container_registry}/muse:${params.MuSE_version}" diff --git a/module/common.nf b/module/common.nf index 4534fe6e..3640e9c0 100644 --- a/module/common.nf +++ b/module/common.nf @@ -5,7 +5,7 @@ log.info """\ Docker Images: - docker_image_BCFtools: ${params.docker_image_BCFtools} - docker_image_validate_params: ${params.docker_image_validate_params} -- docker_image_blarchive: ${params.docker_image_blarchive} +- docker_image_ubuntu: ${params.docker_image_ubuntu} """ process filter_VCF_BCFtools { @@ -90,12 +90,12 @@ process rename_samples_BCFtools { """ } -process compress_file_blarchive { - container params.docker_image_blarchive - publishDir path: params.blarchive_publishDir, +process compress_file_bzip2 { + container params.docker_image_ubuntu + publishDir path: params.compress_publishdir, mode: "copy", pattern: "*.bz2", - enabled: params.blarchive_enabled + enabled: params.compress_enabled publishDir path: "${params.workflow_log_output_dir}", mode: "copy", pattern: ".command.*", @@ -112,8 +112,7 @@ process compress_file_blarchive { """ set -euo pipefail dereferenced_file=\$(readlink -f ${file_to_compress}) - blarchive compress_files --input \$dereferenced_file \ - --log ./ + bzip2 \$dereferenced_file ln -s \${dereferenced_file}.bz2 ${file_to_compress}.bz2 """ } diff --git a/module/intersect.nf b/module/intersect.nf index 83f6d86b..72f8a5fd 100644 --- a/module/intersect.nf +++ b/module/intersect.nf @@ -1,7 +1,7 @@ include { generate_sha512sum } from './common' -include { compress_file_blarchive} from './common' addParams( - blarchive_publishDir : "${params.workflow_output_dir}/output", - blarchive_enabled : true +include { compress_file_bzip2} from './common' addParams( + compress_publishdir : "${params.workflow_output_dir}/output", + compress_enabled : true ) include { reorder_samples_BCFtools; intersect_VCFs_BCFtools; plot_VennDiagram_R; concat_VCFs_BCFtools ; convert_VCF_vcf2maf } from './intersect-processes.nf' include { compress_index_VCF as compress_index_VCF_reordered } from '../external/pipeline-Nextflow-module/modules/common/index_VCF_tabix/main.nf' addParams( @@ -85,7 +85,7 @@ workflow intersect { compress_index_VCF_concat(concat_VCFs_BCFtools.out.vcf .map{ it -> ['SNV', it]} ) - compress_file_blarchive(convert_VCF_vcf2maf.out.maf + compress_file_bzip2(convert_VCF_vcf2maf.out.maf .map{ it -> ['MAF', it]} ) file_for_sha512 = intersect_VCFs_BCFtools.out.gzvcf @@ -101,7 +101,7 @@ workflow intersect { .mix(compress_index_VCF_concat.out.index_out .map{ it -> ["concat-${it[0]}-index", it[2]] } ) - .mix(compress_file_blarchive.out.compressed_file + .mix(compress_file_bzip2.out.compressed_file .map{ it -> ["concat-${it[0]}", it[1]]} ) generate_sha512sum(file_for_sha512) diff --git a/module/somaticsniper.nf b/module/somaticsniper.nf index a4644c6f..69d87b23 100644 --- a/module/somaticsniper.nf +++ b/module/somaticsniper.nf @@ -15,9 +15,9 @@ include { compress_index_VCF as compress_index_VCF_fix } from '../external/pipel bgzip_extra_args: params.bgzip_extra_args, tabix_extra_args: params.tabix_extra_args ]) -include { compress_file_blarchive} from './common' addParams( - blarchive_publishDir : "${params.workflow_output_dir}/intermediate/generate_ReadCount_bam_readcount", - blarchive_enabled : params.save_intermediate_files +include { compress_file_bzip2} from './common' addParams( + compress_publishdir : "${params.workflow_output_dir}/intermediate/generate_ReadCount_bam_readcount", + compress_enabled : params.save_intermediate_files ) workflow somaticsniper { @@ -56,7 +56,7 @@ workflow somaticsniper { filter_FalsePositive_SomaticSniper(apply_TumorIndelFilter_SomaticSniper.out.vcf_tumor, generate_ReadCount_bam_readcount.out.readcount) call_HighConfidenceSNV_SomaticSniper(filter_FalsePositive_SomaticSniper.out.fp_pass) // combining to delay compression until after filtering step - compress_file_blarchive( + compress_file_bzip2( generate_ReadCount_bam_readcount.out.readcount .combine(filter_FalsePositive_SomaticSniper.out.fp_pass.collect()) .map{ it -> ['readcount', it[0]] } From 3c26334704b4784649763f728741971f246b21a4 Mon Sep 17 00:00:00 2001 From: Yash Patel Date: Wed, 18 Oct 2023 18:33:58 -0700 Subject: [PATCH 2/3] Update tests --- config/default.config | 5 +- nftest.yml | 88 ++++++++++++++--------------- test/config/a_mini-all-tools.config | 2 +- test/config/a_mini-mutect2.config | 2 +- 4 files changed, 50 insertions(+), 47 deletions(-) diff --git a/config/default.config b/config/default.config index 8ed710c0..3828774c 100644 --- a/config/default.config +++ b/config/default.config @@ -10,6 +10,9 @@ params { max_cpus = SysHelper.getAvailCpus() max_memory = SysHelper.getAvailMemory() + min_cpus = 1 + min_memory = 1.MB + // default docker container registry docker_container_registry = "ghcr.io/uclahs-cds" @@ -19,7 +22,7 @@ params { GATK_version = "4.4.0.0" somaticsniper_version = "1.0.5.0" bam_readcount_version = "0.8.0" - ubuntu_version = "23.04" + ubuntu_version = "20.04" strelka2_version = "2.9.10" manta_version = "1.6.0" MuSE_version = "2.0.3" diff --git a/nftest.yml b/nftest.yml index 6b4c87e6..b70f5cdc 100644 --- a/nftest.yml +++ b/nftest.yml @@ -14,79 +14,79 @@ cases: skip: false verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh @@ -98,15 +98,15 @@ cases: skip: false verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh @@ -118,15 +118,15 @@ cases: skip: false verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_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 script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_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 script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_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 script: test/assert_vcf.sh @@ -138,51 +138,51 @@ cases: skip: false verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt method: md5 - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh @@ -194,7 +194,7 @@ cases: skip: true verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-somaticsniper/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh @@ -206,11 +206,11 @@ cases: skip: true verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-strelka2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-strelka2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh @@ -222,15 +222,15 @@ cases: skip: true verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh @@ -242,6 +242,6 @@ cases: skip: true verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-muse/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh diff --git a/test/config/a_mini-all-tools.config b/test/config/a_mini-all-tools.config index bf5f9a4a..d56b607d 100644 --- a/test/config/a_mini-all-tools.config +++ b/test/config/a_mini-all-tools.config @@ -28,7 +28,7 @@ params { mutect2_extra_args = '' filter_mutect_calls_extra_args = '' gatk_command_mem_diff = 500.MB - scatter_count = 12 + scatter_count = 50 germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' // MuSE options diff --git a/test/config/a_mini-mutect2.config b/test/config/a_mini-mutect2.config index 8caa770f..398d2f57 100644 --- a/test/config/a_mini-mutect2.config +++ b/test/config/a_mini-mutect2.config @@ -29,7 +29,7 @@ params { mutect2_extra_args = '' filter_mutect_calls_extra_args = '' gatk_command_mem_diff = 500.MB - scatter_count = 12 + scatter_count = 50 germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' // MuSE options From cab723540cfec0dc8029d074e28b1d5c1b7fdf50 Mon Sep 17 00:00:00 2001 From: Yash Patel Date: Wed, 18 Oct 2023 18:35:31 -0700 Subject: [PATCH 3/3] Bump version for release --- CHANGELOG.md | 5 +++ nextflow.config | 2 +- nftest.yml | 88 ++++++++++++++++++++++++------------------------- 3 files changed, 50 insertions(+), 45 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9595a68d..7ecb39e1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +## [7.0.0] - 2023-10-18 + +### Changed +- Use `bzip2` directly for compression + ## [7.0.0-rc.2] - 2023-10-05 ### Added diff --git a/nextflow.config b/nextflow.config index abaa90d8..dfc1633a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,6 +9,6 @@ manifest { nextflowVersion = '>=20.07.1' author = 'Yuan Zhe (Caden) Bugh, Mao Tian, Sorel Fitz-Gibbon' homePage = 'https://github.com/uclahs-cds/pipeline-call-sSNV' - version = '7.0.0-rc.2' + version = '7.0.0' name = 'call-sSNV' } diff --git a/nftest.yml b/nftest.yml index b70f5cdc..bf523666 100644 --- a/nftest.yml +++ b/nftest.yml @@ -14,79 +14,79 @@ cases: skip: false verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-all-tools-std-input/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh @@ -98,15 +98,15 @@ cases: skip: false verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh @@ -118,15 +118,15 @@ cases: skip: false verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_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 script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_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 script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_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 script: test/assert_vcf.sh @@ -138,51 +138,51 @@ cases: skip: false verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2 method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt method: md5 - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz script: test/assert_vcf.sh @@ -194,7 +194,7 @@ cases: skip: true verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-somaticsniper/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh @@ -206,11 +206,11 @@ cases: skip: true verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-strelka2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-strelka2/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh @@ -222,15 +222,15 @@ cases: skip: true verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_MNV.vcf.gz script: test/assert_vcf.sh - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2/TWGSAMIN000001-T001-S01-F/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh @@ -242,6 +242,6 @@ cases: skip: true verbose: true asserts: - - actual: call-sSNV-7.0.0-rc.2/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz + - actual: call-sSNV-7.0.0/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/output/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-muse/TWGSAMIN000001-T001-S01-F/MuSE-2.0.3/MuSE-2.0.3_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz script: test/assert_vcf.sh