From b8a6347b54efd5b9464eaeca65a2ed792b99ac31 Mon Sep 17 00:00:00 2001 From: Yash Patel <86321070+yashpatel6@users.noreply.github.com> Date: Tue, 12 Mar 2024 13:17:12 -0700 Subject: [PATCH] Update testing sample for `v6.0.0-rc.1` (#170) * Switch align-DNA test to Illumina sample * Update BAM2FASTQ test * Update sample for recalibrate-BAM * Update sample for calculate-targeted-coverage * Update tests for call-gSNP and call-sSNV * Update samples for call-gSNP and call-sSNV * Update sample for call-mtSNV * Update sample for call-gSV * Update sample for call-sSV * Update test cases * Update sample for sCNA * Update metapipeline_dna.nf test * Add sCNA assertion back * Update BAM entry batch test * Update FASTQ input test * Update CHANGELOG * Update nextflow.config * Update to common paths --- CHANGELOG.md | 5 + module/call_sSV/create_YAML_call_sSV.nf | 5 - nextflow.config | 4 +- nftest.yaml | 166 +++++++----------- test/test-align-DNA/test.config | 48 ++--- test/test-bam2fastq/input.csv | 2 +- test/test-bam2fastq/test.config | 6 +- .../test.config | 10 +- test/test-call-gSNP/test.config | 16 +- test/test-call-gSV/test.config | 19 +- test/test-call-mtSNV/test.config | 16 +- test/test-call-sCNA/test-cnv_facets.config | 16 +- test/test-call-sSNV/test.config | 18 +- test/test-call-sSV/test.config | 18 +- test/test-metapipeline-DNA-batch/input.csv | 4 + test/test-metapipeline-DNA-batch/test.config | 17 +- .../input.yaml | 68 +++---- .../test.config | 6 +- test/test-metapipeline-DNA/input.csv | 4 +- .../pipeline_specific_params.json | 14 +- test/test-metapipeline-DNA/test.config | 4 +- test/test-recalibrate-BAM/test.config | 16 +- 22 files changed, 236 insertions(+), 246 deletions(-) create mode 100644 test/test-metapipeline-DNA-batch/input.csv diff --git a/CHANGELOG.md b/CHANGELOG.md index 64aeea2a..55309e2f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm --- ## [Unreleased] + +--- + +## [6.0.0-rc.1] - 2024-03-11 ### Added + pipeline-call-sCNA `v3.0.0` and its NFTest + Targeted coverage pipeline @@ -18,6 +22,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm + Sanitize metadata passed to align-DNA + Calculate-targeted-coverage: update name from targeted-coverage + Save logs and input files for all pipelines ++ Update test samples --- diff --git a/module/call_sSV/create_YAML_call_sSV.nf b/module/call_sSV/create_YAML_call_sSV.nf index 838e2c44..af5dde99 100644 --- a/module/call_sSV/create_YAML_call_sSV.nf +++ b/module/call_sSV/create_YAML_call_sSV.nf @@ -9,11 +9,6 @@ import org.yaml.snakeyaml.Yaml * @return A path to the input YAML */ process create_YAML_call_sSV { - publishDir path: "${params.log_output_dir}/process-log", - mode: "copy", - pattern: ".command.*", - saveAs: { "${task.process}-${tumor_id}/log${file(it).getName()}" } - publishDir "${params.output_dir}/intermediate/${task.process.replace(':', '/')}-${tumor_id}", pattern: 'call_sSV_input.yaml', mode: 'copy' diff --git a/nextflow.config b/nextflow.config index 3d5cf26a..b9779f36 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,7 +1,7 @@ // Metadata manifest { name = 'metapipeline-DNA' - author = ['Yash Patel', 'Chenghao Zhu', 'Helena Winata', 'Alfredo Enrique Gonzalez', 'Nicholas Wang', 'Mohammed Faizal Eeman Mootor'] + author = ['Yash Patel', 'Chenghao Zhu', 'Helena Winata', 'Alfredo Enrique Gonzalez', 'Nicholas Wang', 'Sorel Fitz-Gibbon', 'Mohammed Faizal Eeman Mootor', 'Nicole Zeltser'] description = 'Nextflow pipeline to convert BAM to FASTQ, align, call gSNP, call sSNV, call gSV, call sSV and call mtSNV' - version = '5.3.1' + version = '6.0.0-rc.1' } diff --git a/nftest.yaml b/nftest.yaml index e08ee150..09f30012 100644 --- a/nftest.yaml +++ b/nftest.yaml @@ -13,12 +13,11 @@ cases: verbose: true skip: true asserts: - - actual: output/convert-BAM2FASTQ-*/TCEB1_RCC_S00-9422N_079_114/SAMtools-*/output/S00-9422N_079_114.Seq1_collated_R1.fq.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/bam2fastq/output/TCEB1/TCEB1_RCC_S00-9422N_079_114/collated_S00-9422N_079_114.Seq1_R1.fq.gz + - actual: output/convert-BAM2FASTQ-*/NA24149/SAMtools-*/output/NA24149RG.Seq1_collated_R1.fq.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/convert-BAM2FASTQ-2.0.0-rc.2/NA24149/SAMtools-1.15.1/output/NA24149RG.Seq1_collated_R1.fq.gz script: test/test-bam2fastq/assert_fastq.sh - - - actual: output/convert-BAM2FASTQ-*/TCEB1_RCC_S00-9422N_079_114/SAMtools-*/output/S00-9422N_079_114.Seq1_collated_R2.fq.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/bam2fastq/output/TCEB1/TCEB1_RCC_S00-9422N_079_114/collated_S00-9422N_079_114.Seq1_R2.fq.gz + - actual: output/convert-BAM2FASTQ-*/NA24149/SAMtools-*/output/NA24149RG.Seq1_collated_R2.fq.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/convert-BAM2FASTQ-2.0.0-rc.2/NA24149/SAMtools-1.15.1/output/NA24149RG.Seq1_collated_R2.fq.gz script: test/test-bam2fastq/assert_fastq.sh - name: test-align-DNA @@ -28,14 +27,6 @@ cases: verbose: true skip: true # Disabling BAM comparisons since there can be variability based on number of threads used - # asserts: - # - actual: output/align-DNA-9.0.0/TCEB1-RCC-S00-9422N-079-114/BWA-MEM2-2.2.1/output/BWA-MEM2-2.2.1_TCEB1_TCEB1-RCC-S00-9422N-079-114.bam - # expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/align-DNA/TCEB1/TCEB1_RCC_S00-9422N_079_114/TCEB1_RCC_S00-9422N_079_114.bam - # method: md5 - - # - actual: output/align-DNA-9.0.0/TCEB1-RCC-S00-9422T-027-166/BWA-MEM2-2.2.1/output/BWA-MEM2-2.2.1_TCEB1_TCEB1-RCC-S00-9422T-027-166.bam - # expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/align-DNA/TCEB1/TCEB1_RCC_S00-9422T_027_166/TCEB1_RCC_S00-9422T_027_166.bam - # method: md5 - name: test-recalibrate-BAM message: Test recalibrate-BAM @@ -51,14 +42,14 @@ cases: verbose: true skip: true asserts: - - actual: output/calculate-targeted-coverage-1.0.0-rc.2/9422N/SAMtools-1.16.1/output/9422N.collapsed_coverage.bed - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-calculate-targeted-coverage/9422N/SAMtools-1.16.1/output/9422N.collapsed_coverage.bed + - actual: output/calculate-targeted-coverage-*/NA24149/SAMtools-*/output/NA24149.collapsed_coverage.bed + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/calculate-targeted-coverage-1.0.0-rc.2/NA24149/SAMtools-1.16.1/output/NA24149.collapsed_coverage.bed script: test/test-calculate-targeted-coverage/assert_bed.sh - - actual: output/calculate-targeted-coverage-1.0.0-rc.2/9422N/SAMtools-1.16.1/output/9422N.off-target-dbSNP_depth-per-base.bed - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-calculate-targeted-coverage/9422N/SAMtools-1.16.1/output/9422N.off-target-dbSNP_depth-per-base.bed + - actual: output/calculate-targeted-coverage-*/NA24149/SAMtools-*/output/NA24149.off-target-dbSNP_depth-per-base.bed + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/calculate-targeted-coverage-1.0.0-rc.2/NA24149/SAMtools-1.16.1/output/NA24149.off-target-dbSNP_depth-per-base.bed script: test/test-calculate-targeted-coverage/assert_bed.sh - - actual: output/calculate-targeted-coverage-1.0.0-rc.2/9422N/SAMtools-1.16.1/output/9422N.target_with_enriched_off-target_intervals.bed - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-calculate-targeted-coverage/9422N/SAMtools-1.16.1/output/9422N.target_with_enriched_off-target_intervals.bed + - actual: output/calculate-targeted-coverage-*/NA24149/SAMtools-*/output/NA24149.target_with_enriched_off-target_intervals.bed + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/calculate-targeted-coverage-1.0.0-rc.2/NA24149/SAMtools-1.16.1/output/NA24149.target_with_enriched_off-target_intervals.bed script: test/test-calculate-targeted-coverage/assert_bed.sh - name: test-call-gSNP @@ -68,15 +59,12 @@ cases: verbose: true skip: true asserts: - - actual: output/call-gSNP-10.0.0-rc.3/9422T/GATK-4.2.4.1/output/GATK-4.2.4.1_test_S00-9422T-027-166.g.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/output/test-call-gSNP/TCEB1/GATK-4.2.4.1_test_S00-9422T-027-166.g.vcf.gz + - actual: output/call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143.g.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSNP-10.0.0-rc.3/NA24143/GATK-4.2.4.1/output/GATK-*_IlluminaTest_NA24143.g.vcf.gz + script: test/test-call-gSNP/assert_vcf.sh + - actual: output/call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24149.g.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSNP-10.0.0-rc.3/NA24143/GATK-4.2.4.1/output/GATK-*_IlluminaTest_NA24149.g.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - # Disabling BAM comparison for now - checksums differ even if tools like GATK CompareSAMs report identical BAM files - # requires a custom script to use GATK docker for comparison of BAMs - # - actual: test/output/output/call-gSNP-8.0.0/TCEB1_RCC_S00/GATK-4.2.4.1/output/S00-9422N_079_114_realigned_recalibrated_merged.bam - # expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/output/test-call-gSNP/TCEB1/S00-9422N_079_114_realigned_recalibrated_merged.bam - - name: test-call-sSNV message: Test call-sSNV with one tumor normal pair @@ -85,44 +73,43 @@ cases: verbose: true skip: true asserts: - - actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/BCFtools-1.17_LUAD0000034_CPT0053040010_SNV-concat.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/BCFtools-1.17_LUAD0000034_CPT0053040010_SNV-concat.vcf.gz + - actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/BCFtools-*_IlluminaTest_NA24143_SNV-concat.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/BCFtools-1.17_IlluminaTest_NA24143_SNV-concat.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/MuSE-2.0.4_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/MuSE-2.0.4_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz + - actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/MuSE-*_IlluminaTest_NA24143_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/MuSE-2.0.4_IlluminaTest_NA24143_SNV-intersect.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz + - actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/Mutect2-*_IlluminaTest_NA24143_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_IlluminaTest_NA24143_SNV-intersect.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/SomaticSniper-1.0.5.0_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz + - actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/SomaticSniper-*_IlluminaTest_NA24143_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_IlluminaTest_NA24143_SNV-intersect.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Strelka2-2.9.10_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz + - actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/Strelka2-*_IlluminaTest_NA24143_SNV-intersect.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_IlluminaTest_NA24143_SNV-intersect.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/MuSE-2.0.4/output/MuSE-2.0.4_LUAD0000034_CPT0053040010_SNV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/MuSE-2.0.4_LUAD0000034_CPT0053040010_SNV.vcf.gz + - actual: output/call-sSNV-*/NA24143/MuSE-*/output/MuSE-*_IlluminaTest_NA24143_SNV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/MuSE-2.0.4/output/MuSE-2.0.4_IlluminaTest_NA24143_SNV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_LUAD0000034_CPT0053040010_SNV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/SomaticSniper-1.0.5.0_LUAD0000034_CPT0053040010_SNV.vcf.gz + - actual: output/call-sSNV-*/NA24143/SomaticSniper-*/output/SomaticSniper-*_IlluminaTest_NA24143_SNV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_IlluminaTest_NA24143_SNV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_CPT0053040010_Indel.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Strelka2-2.9.10_LUAD0000034_CPT0053040010_Indel.vcf.gz + - actual: output/call-sSNV-*/NA24143/Strelka2-*/output/Strelka2-*_IlluminaTest_NA24143_Indel.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Strelka2-2.9.10/output/Strelka2-2.9.10_IlluminaTest_NA24143_Indel.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_CPT0053040010_SNV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Strelka2-2.9.10_LUAD0000034_CPT0053040010_SNV.vcf.gz + - actual: output/call-sSNV-*/NA24143/Strelka2-*/output/Strelka2-*_IlluminaTest_NA24143_SNV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Strelka2-2.9.10/output/Strelka2-2.9.10_IlluminaTest_NA24143_SNV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_Indel.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_Indel.vcf.gz + - actual: output/call-sSNV-*/NA24143/Mutect2-*/output/Mutect2-*_IlluminaTest_NA24143_Indel.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_IlluminaTest_NA24143_Indel.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_MNV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_MNV.vcf.gz + - actual: output/call-sSNV-*/NA24143/Mutect2-*/output/Mutect2-*_IlluminaTest_NA24143_MNV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_IlluminaTest_NA24143_MNV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSNV-*/CPT0053040010/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_SNV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_SNV.vcf.gz + - actual: output/call-sSNV-*/NA24143/Mutect2-*/output/Mutect2-*_IlluminaTest_NA24143_SNV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_IlluminaTest_NA24143_SNV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - name: test-call-mtSNV message: Test call-mtSNV pipeline with one tumor normal pair nf_script: test/test-call-mtSNV/test.nf @@ -130,18 +117,18 @@ cases: verbose: true skip: true asserts: - # Disabling the tsv test as the tsv contains a timestamp so files are never equal - might require a custom comparison script - # - actual: test/output/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_mtSNV/call_heteroplasmy/GZLUCPTA000001-T001-P01-F_vs_GZLUCPTA000001-N001-B01-F.tsv - # expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-mtSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_mtSNV/call_heteroplasmy/GZLUCPTA000001-T001-P01-F_vs_GZLUCPTA000001-N001-B01-F.tsv - - - actual: output/call-mtSNV-3.0.0/GZLUCPTA000001-T001-P01-F/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_LUAD0000034_GZLUCPTA000001-N001-B01-F.vcf - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-mtSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_mtSNV/convert_mitoCaller2vcf_mitoCaller/GZLUCPTA000001-T001-P01-F/GZLUCPTA000001-T001-P01-F.vcf + - actual: output/call-mtSNV-*/NA24143/mitoCaller-*/output/mitoCaller2vcf-*_IlluminaTest_NA24143.vcf + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-mtSNV-3.0.0/NA24143/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_IlluminaTest_NA24143.vcf script: test/test-call-gSNP/assert_vcf.sh - - - actual: output/call-mtSNV-3.0.0/GZLUCPTA000001-T001-P01-F/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_LUAD0000034_GZLUCPTA000001-N001-B01-F_homoplasmy.vcf - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-mtSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_mtSNV/convert_mitoCaller2vcf_mitoCaller/GZLUCPTA000001-T001-P01-F/GZLUCPTA000001-T001-P01-F_homoplasmy.vcf + - actual: output/call-mtSNV-*/NA24143/mitoCaller-*/output/mitoCaller2vcf-*_IlluminaTest_NA24143_homoplasmy.vcf + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-mtSNV-3.0.0/NA24143/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_IlluminaTest_NA24143_homoplasmy.vcf + script: test/test-call-gSNP/assert_vcf.sh + - actual: output/call-mtSNV-*/NA24143/mitoCaller-*/output/mitoCaller2vcf-*_IlluminaTest_NA24149.vcf + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-mtSNV-3.0.0/NA24143/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_IlluminaTest_NA24149.vcf + script: test/test-call-gSNP/assert_vcf.sh + - actual: output/call-mtSNV-*/NA24143/mitoCaller-*/output/mitoCaller2vcf-*_IlluminaTest_NA24149_homoplasmy.vcf + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-mtSNV-3.0.0/NA24143/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_IlluminaTest_NA24149_homoplasmy.vcf script: test/test-call-gSNP/assert_vcf.sh - - name: test-call-gSV message: Test call-gSV pipeline with one tumor normal pair @@ -150,23 +137,16 @@ cases: verbose: true skip: true asserts: - - actual: output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/DELLY-1.1.3/output/DELLY-1.1.3_CNV_LUAD0000034_GZLUCPTA000001-N001-B01-F.bcf - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-gSV/output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/DELLY-1.1.3/output/DELLY-1.1.3_CNV_LUAD0000034_GZLUCPTA000001-N001-B01-F.bcf - script: test/test-call-gSV/assert_bcf.sh - - actual: output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/DELLY-1.1.3/output/DELLY-1.1.3_SV_LUAD0000034_GZLUCPTA000001-N001-B01-F.bcf - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-gSV/output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/DELLY-1.1.3/output/DELLY-1.1.3_SV_LUAD0000034_GZLUCPTA000001-N001-B01-F.bcf - script: test/test-call-gSV/assert_bcf.sh - - actual: output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/Manta-1.6.0/output/diploidSV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-gSV/output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/Manta-1.6.0/output/diploidSV.vcf.gz + - actual: output/call-gSV-*/NA24149/Manta-*/output/diploidSV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSV-4.0.1/NA24149/Manta-1.6.0/output/diploidSV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/Manta-1.6.0/output/candidateSV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-gSV/output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/Manta-1.6.0/output/candidateSV.vcf.gz + - actual: output/call-gSV-*/NA24149/Manta-*/output/candidateSV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSV-4.0.1/NA24149/Manta-1.6.0/output/candidateSV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/Manta-1.6.0/output/candidateSmallIndels.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-gSV/output/call-gSV-4.0.1/GZLUCPTA000001-N001-B01-F/Manta-1.6.0/output/candidateSmallIndels.vcf.gz + - actual: output/call-gSV-*/NA24149/Manta-*/output/candidateSmallIndels.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSV-4.0.1/NA24149/Manta-1.6.0/output/candidateSmallIndels.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - name: test-call-sSV message: Test call-sSV pipeline with one tumor normal pair nf_script: test/test-call-sSV/test.nf @@ -174,20 +154,20 @@ cases: verbose: true skip: true asserts: - - actual: output/call-sSV-6.0.0-rc.1/CPT0053040010/DELLY-1.1.3/output/DELLY-1.1.3_LUAD0000034_CPT0053040010.bcf - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-sSV/output/call-sSV-5.0.0/CPT0053040010_realigned_recalibrated_reheadered/DELLY-1.1.3/output/DELLY-1.1.3_LUAD0000034_CPT0053040010-realigned-recalibrated-reheadered.bcf + - actual: output/call-sSV-*/NA24143/DELLY-*/output/DELLY-*_IlluminaTest_NA24143.bcf + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.0.0-rc.1/NA24143/DELLY-1.1.3/output/DELLY-1.1.3_IlluminaTest_NA24143.bcf script: test/test-call-gSV/assert_bcf.sh - - actual: output/call-sSV-6.0.0-rc.1/CPT0053040010/Manta-1.6.0/output/Manta-1.6.0_LUAD0000034_CPT0053040010_diploidSV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-sSV/output/call-sSV-5.0.0/CPT0053040010_realigned_recalibrated_reheadered/Manta-1.6.0/output/Manta-1.6.0_LUAD0000034_CPT0053040010-realigned-recalibrated-reheadered_diploidSV.vcf.gz + - actual: output/call-sSV-*/NA24143/Manta-*/output/Manta-*_IlluminaTest_NA24143_diploidSV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.0.0-rc.1/NA24143/Manta-1.6.0/output/Manta-1.6.0_IlluminaTest_NA24143_diploidSV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSV-6.0.0-rc.1/CPT0053040010/Manta-1.6.0/output/Manta-1.6.0_LUAD0000034_CPT0053040010_candidateSV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-sSV/output/call-sSV-5.0.0/CPT0053040010_realigned_recalibrated_reheadered/Manta-1.6.0/output/Manta-1.6.0_LUAD0000034_CPT0053040010-realigned-recalibrated-reheadered_candidateSV.vcf.gz + - actual: output/call-sSV-*/NA24143/Manta-*/output/Manta-*_IlluminaTest_NA24143_candidateSV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.0.0-rc.1/NA24143/Manta-1.6.0/output/Manta-1.6.0_IlluminaTest_NA24143_candidateSV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSV-6.0.0-rc.1/CPT0053040010/Manta-1.6.0/output/Manta-1.6.0_LUAD0000034_CPT0053040010_candidateSmallIndels.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-sSV/output/call-sSV-5.0.0/CPT0053040010_realigned_recalibrated_reheadered/Manta-1.6.0/output/Manta-1.6.0_LUAD0000034_CPT0053040010-realigned-recalibrated-reheadered_candidateSmallIndels.vcf.gz + - actual: output/call-sSV-*/NA24143/Manta-*/output/Manta-*_IlluminaTest_NA24143_candidateSmallIndels.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.0.0-rc.1/NA24143/Manta-1.6.0/output/Manta-1.6.0_IlluminaTest_NA24143_candidateSmallIndels.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - actual: output/call-sSV-6.0.0-rc.1/CPT0053040010/Manta-1.6.0/output/Manta-1.6.0_LUAD0000034_CPT0053040010_somaticSV.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-sSV/output/call-sSV-5.0.0/CPT0053040010_realigned_recalibrated_reheadered/Manta-1.6.0/output/Manta-1.6.0_LUAD0000034_CPT0053040010-realigned-recalibrated-reheadered_somaticSV.vcf.gz + - actual: output/call-sSV-*/NA24143/Manta-*/output/Manta-*_IlluminaTest_NA24143_somaticSV.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.0.0-rc.1/NA24143/Manta-1.6.0/output/Manta-1.6.0_IlluminaTest_NA24143_somaticSV.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - name: test-call-sCNA-cnv-facets @@ -197,20 +177,10 @@ cases: verbose: true skip: true asserts: - - actual: output/call-sCNA-*/CPT0053040010/cnv_facets-*/output/CNV-FACETS-*_LUAD0000034_CPT0053040010.vcf.gz - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-sCNA/CPT0053040010/cnv_facets-0.16.0/output/CNV-FACETS-0.16.0_LUAD0000034_CPT0053040010.vcf.gz + - actual: output/call-sCNA-*/NA24143/cnv_facets-*/output/CNV-FACETS-*_IlluminaTest_NA24143.vcf.gz + expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sCNA-cnv-facets-3.0.0/NA24143/cnv_facets-0.16.0/output/CNV-FACETS-0.16.0_IlluminaTest_NA24143.vcf.gz script: test/test-call-gSNP/assert_vcf.sh - - - name: test-call-sCNA-battenberg - message: Test call-sCNA pipeline with one tumor normal pair and Battenberg as the CNA caller - nf_script: test/test-call-sCNA/test.nf - nf_config: test/test-call-sCNA/test-Battenberg.config - verbose: true - skip: true - asserts: - - actual: output/call-sCNA-*/ILHNLNEV000002-T001-P01-F/Battenberg-*/output/Battenberg-*_HNSC0000016_ILHNLNEV000002-T001-P01-F_subclones.txt - expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/5.0.0-rc.4/test-output/test-call-sCNA/ILHNLNEV000002-T001-P01-F/Battenberg-2.2.9/output/Battenberg-2.2.9_HNSC0000016_ILHNLNEV000002-T001-P01-F_subclones.txt - script: md5 + # TO-DO: Add Battenberg test sample - name: test-metapipeline-DNA message: Test calling all pipelines with one tumor normal pair diff --git a/test/test-align-DNA/test.config b/test/test-align-DNA/test.config index 787ca7ba..14e943c2 100644 --- a/test/test-align-DNA/test.config +++ b/test/test-align-DNA/test.config @@ -1,8 +1,8 @@ params { work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'GZLUCPTA000001' - project_id = 'LUAD0000034' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'paired' override_realignment = false @@ -26,36 +26,36 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-align-DNA" params.sample_data = [ - 'TCEB1-RCC-S00-9422T-027-166': [ - 'patient': 'TCEB1', + 'NA24143': [ + 'patient': 'IlluminaPatient1', 'state': 'tumor', 'align-DNA': ['BWA-MEM2': ['BAM':'']], 'original_data': [[ - 'read_group_identifier': 'S00-9422T_027_166.Seq1', - 'sequencing_center': 'S00-9422T_027_166_NoIndex', - 'library_identifier': 'S00-9422T_027_166_NoIndex', - 'platform_technology': 'ILLUMINA', - 'platform_unit': 'S00-9422T_027_166_NoIndex_L003', - 'bam_header_sm': 'S00-9422T_027_166', - 'lane': 0, - 'read1_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/S00-9422T_027_166/collated_S00-9422T_027_166.Seq1_R1.fq.gz', - 'read2_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/S00-9422T_027_166/collated_S00-9422T_027_166.Seq1_R2.fq.gz' + 'read_group_identifier': 'NA24143RG', + 'sequencing_center': 'Illumina', + 'library_identifier': 'NA24143LIB', + 'platform_technology': 'Illumina', + 'platform_unit': 'Platform1', + 'bam_header_sm': 'NA24143', + 'lane': 1, + 'read1_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24143/IDPE2plus-NA24143-R4-MitoEx-1to100_S21_L001_R1_001.fastq.gz', + 'read2_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24143/IDPE2plus-NA24143-R4-MitoEx-1to100_S21_L001_R2_001.fastq.gz' ]] ], - 'TCEB1-RCC-S00-9422N-079-114': [ - 'patient': 'TCEB1', + 'NA24149': [ + 'patient': 'IlluminaPatient1', 'state': 'normal', 'align-DNA': ['BWA-MEM2': ['BAM':'']], 'original_data': [[ - 'read_group_identifier': 'S00-9422N_079_114.Seq1', - 'sequencing_center': 'S00-9422N_079_114_NoIndex', - 'library_identifier': 'S00-9422N_079_114_NoIndex', - 'platform_technology': 'ILLUMINA', - 'platform_unit': 'S00-9422N_079_114_NoIndex_L003', - 'bam_header_sm': 'S00-9422N_079_114', - 'lane': 0, - 'read1_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/S00-9422N_079_114/collated_S00-9422N_079_114.Seq1_R1.fq.gz', - 'read2_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/S00-9422N_079_114/collated_S00-9422N_079_114.Seq1_R2.fq.gz' + 'read_group_identifier': 'NA24149RG', + 'sequencing_center': 'Illumina', + 'library_identifier': 'NA24149LIB', + 'platform_technology': 'Illumina', + 'platform_unit': 'Platform1', + 'bam_header_sm': 'NA24149', + 'lane': 1, + 'read1_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24149/IDPE2plus-NA24149-R3-MitoEx-1to1000_S41_L001_R1_001.fastq.gz', + 'read2_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24149/IDPE2plus-NA24149-R3-MitoEx-1to1000_S41_L001_R2_001.fastq.gz' ]] ] ] diff --git a/test/test-bam2fastq/input.csv b/test/test-bam2fastq/input.csv index ca648018..754db069 100644 --- a/test/test-bam2fastq/input.csv +++ b/test/test-bam2fastq/input.csv @@ -1,2 +1,2 @@ patient,sample,state,bam -TCEB1,TCEB1_RCC_S00-9422N_079_114,normal,/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/bam2fastq/inputs/TCEB1_RCC_S00-9422N_079_114_merged_05prcnt.bam +IlluminaPatient1,NA24149,normal,/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24149.bam diff --git a/test/test-bam2fastq/test.config b/test/test-bam2fastq/test.config index 46c91b63..efe3221c 100644 --- a/test/test-bam2fastq/test.config +++ b/test/test-bam2fastq/test.config @@ -2,8 +2,8 @@ params { input_csv = "${launchDir}/test/test-bam2fastq/input.csv" work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'GZLUCPTA000001' - project_id = 'LUAD0000034' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'paired' override_realignment = false @@ -24,7 +24,7 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-convert-BAM2FASTQ" params.sample_data = [ - 'TCEB1_RCC_S00-9422N_079_114': [ + 'NA24149': [ 'convert-BAM2FASTQ': [] ] ] diff --git a/test/test-calculate-targeted-coverage/test.config b/test/test-calculate-targeted-coverage/test.config index 26d6e8ee..840e6892 100644 --- a/test/test-calculate-targeted-coverage/test.config +++ b/test/test-calculate-targeted-coverage/test.config @@ -3,8 +3,8 @@ import nextflow.util.SysHelper params { work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'TCEB1' - project_id = 'test' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'single' calculate_targeted_coverage { @@ -30,10 +30,10 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-calculate-targeted-coverage" params.sample_data = [ - '9422N': [ - 'patient': 'TCEB1_RCC_S00', + 'NA24149': [ + 'patient': 'IlluminaPatient1', 'state': 'normal', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/inputs/TCEB1/TCEB1_RCC_S00-9422N-079-114.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':''] ] ] diff --git a/test/test-call-gSNP/test.config b/test/test-call-gSNP/test.config index c082300b..e15a4f6a 100644 --- a/test/test-call-gSNP/test.config +++ b/test/test-call-gSNP/test.config @@ -3,8 +3,8 @@ import nextflow.util.SysHelper params { work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'TCEB1' - project_id = 'test' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'paired' call_gSNP { @@ -28,15 +28,15 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-gSNP" params.sample_data = [ - '9422T': [ - 'patient': 'TCEB1_RCC_S00', + 'NA24143': [ + 'patient': 'IlluminaPatient1', 'state': 'tumor', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/inputs/TCEB1/TCEB1_RCC_S00-9422T_027_166.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':''] ], - '9422N': [ - 'patient': 'TCEB1_RCC_S00', + 'NA24149': [ + 'patient': 'IlluminaPatient1', 'state': 'normal', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/inputs/TCEB1/TCEB1_RCC_S00-9422N-079-114.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':''] ] ] diff --git a/test/test-call-gSV/test.config b/test/test-call-gSV/test.config index ef3f63f3..d788649c 100644 --- a/test/test-call-gSV/test.config +++ b/test/test-call-gSV/test.config @@ -1,15 +1,16 @@ params { work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'GZLUCPTA000001' - project_id = 'LUAD0000034' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'paired' call_gSV { subworkflow_cpus = 8 - reference_fasta = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/downsampled_data/genome/genome.fa' + reference_fasta = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' exclusion_file = '/hot/ref/tool-specific-input/Delly/GRCh38/human.hg38.excl.tsv' mappability_map = '/hot/ref/tool-specific-input/Delly/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz' + run_delly = false } arg_map = [:] @@ -22,15 +23,15 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-gSV" params.sample_data = [ - 'GZLUCPTA000001-T001-P01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24143': [ + 'patient': 'IlluminaPatient1', 'state': 'tumor', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':''] ], - 'GZLUCPTA000001-N001-B01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24149': [ + 'patient': 'IlluminaPatient1', 'state': 'normal', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':''] ] ] diff --git a/test/test-call-mtSNV/test.config b/test/test-call-mtSNV/test.config index 7fdda826..7734b5e2 100644 --- a/test/test-call-mtSNV/test.config +++ b/test/test-call-mtSNV/test.config @@ -1,8 +1,8 @@ params { work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'GZLUCPTA000001' - project_id = 'LUAD0000034' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'paired' call_mtSNV { @@ -21,15 +21,15 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-mtSNV" params.sample_data = [ - 'GZLUCPTA000001-T001-P01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24143': [ + 'patient': 'IlluminaPatient1', 'state': 'tumor', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':''] ], - 'GZLUCPTA000001-N001-B01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24149': [ + 'patient': 'IlluminaPatient1', 'state': 'normal', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':''] ] ] diff --git a/test/test-call-sCNA/test-cnv_facets.config b/test/test-call-sCNA/test-cnv_facets.config index 9a3cc2a0..4d0521ce 100644 --- a/test/test-call-sCNA/test-cnv_facets.config +++ b/test/test-call-sCNA/test-cnv_facets.config @@ -1,8 +1,8 @@ params { work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'GZLUCPTA000001' - project_id = 'LUAD0000034' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'paired' call_sCNA { @@ -25,15 +25,15 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-sCNA" params.sample_data = [ - 'GZLUCPTA000001-T001-P01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24143': [ + 'patient': 'IlluminaPatient1', 'state': 'tumor', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':''] ], - 'GZLUCPTA000001-N001-B01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24149': [ + 'patient': 'IlluminaPatient1', 'state': 'normal', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':''] ] ] diff --git a/test/test-call-sSNV/test.config b/test/test-call-sSNV/test.config index 116ee707..6da5d106 100644 --- a/test/test-call-sSNV/test.config +++ b/test/test-call-sSNV/test.config @@ -1,15 +1,15 @@ params { work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'GZLUCPTA000001' - project_id = 'LUAD0000034' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'paired' call_sSNV { subworkflow_cpus = 8 algorithm = ['somaticsniper', 'strelka2', 'mutect2', 'muse'] - reference = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/downsampled_data/genome/genome.fa' + reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' exome = false intersect_regions = "${launchDir}/test/test-call-sSNV/Homo_sapiens_assembly38_no-decoy_downsampled.bed.gz" germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' @@ -27,15 +27,15 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-sSNV" params.sample_data = [ - 'GZLUCPTA000001-T001-P01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24143': [ + 'patient': 'IlluminaPatient1', 'state': 'tumor', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':''] ], - 'GZLUCPTA000001-N001-B01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24149': [ + 'patient': 'IlluminaPatient1', 'state': 'normal', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':''] ] ] diff --git a/test/test-call-sSV/test.config b/test/test-call-sSV/test.config index 5c328d64..7492dd66 100644 --- a/test/test-call-sSV/test.config +++ b/test/test-call-sSV/test.config @@ -1,13 +1,13 @@ params { work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'GZLUCPTA000001' - project_id = 'LUAD0000034' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'paired' call_sSV { subworkflow_cpus = 8 - reference_fasta = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/downsampled_data/genome/genome.fa' + reference_fasta = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' algorithm = ['delly', 'manta'] exclusion_file = '/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv' } @@ -22,15 +22,15 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-sSV" params.sample_data = [ - 'GZLUCPTA000001-T001-P01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24143': [ + 'patient': 'IlluminaPatient1', 'state': 'tumor', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':''] ], - 'GZLUCPTA000001-N001-B01-F': [ - 'patient': 'GZLUCPTA000001', + 'NA24149': [ + 'patient': 'IlluminaPatient1', 'state': 'normal', - 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':''] + 'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':''] ] ] diff --git a/test/test-metapipeline-DNA-batch/input.csv b/test/test-metapipeline-DNA-batch/input.csv new file mode 100644 index 00000000..855150a0 --- /dev/null +++ b/test/test-metapipeline-DNA-batch/input.csv @@ -0,0 +1,4 @@ +patient,sample,state,path +IlluminaPatient1,NA24143,tumor,/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24143.bam +IlluminaPatient1,NA24149,normal,/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24149.bam +IlluminaPatient1,NA24385,tumor,/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24385/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24385.bam diff --git a/test/test-metapipeline-DNA-batch/test.config b/test/test-metapipeline-DNA-batch/test.config index 05165553..35e52a1e 100644 --- a/test/test-metapipeline-DNA-batch/test.config +++ b/test/test-metapipeline-DNA-batch/test.config @@ -3,10 +3,10 @@ includeConfig "${projectDir}/config/methods.config" includeConfig "${projectDir}/nextflow.config" params { - input_csv = "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/csv/multi_sample/targeted_panel_multi.csv" + input_csv = ("${projectDir}/test/test-metapipeline-DNA-batch/input.csv" as String) leading_work_dir = "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/common_work_dir" pipeline_work_dir = '/scratch' //For individual pipeline outputs before copying to output_dir - project_id = 'BZPRGPT1' + project_id = 'IlluminaTest' save_intermediate_files = true partition = 'F32' @@ -71,6 +71,7 @@ params { reference_fasta = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' exclusion_file = '/hot/ref/tool-specific-input/Delly/GRCh38/human.hg38.excl.tsv' mappability_map = '/hot/ref/tool-specific-input/Delly/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz' + run_delly = false } call_sSV { @@ -79,6 +80,18 @@ params { exclusion_file = '/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv' } + calculate_targeted_coverage { + reference_dict = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict' + reference_dbSNP = '/hot/ref/database/dbSNP-155/thinned/GRCh38/dbSNP-155_thinned_hg38.vcf.gz' + genome_sizes = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai' + target_bed = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/targeted-coverage/small.bed' //required + bait_bed = '' //optional, path/to/bait/bedfile + collect_metrics = true // whether or not to calculate coverage metrics + off_target_depth = true //whether or not to calculate depth at off-target dbSNP loci + output_enriched_target_file = true // whether or not to output a new target file containing high-coverage off-target dbSNP loci + target_depth = false // whether or not to calculate per-base depth in target regions + } + call_sCNA { subworkflow_cpus = 8 algorithm = ['cnv_facets'] diff --git a/test/test-metapipeline-DNA-fastq-input/input.yaml b/test/test-metapipeline-DNA-fastq-input/input.yaml index 1fc2bec2..b77dcaed 100644 --- a/test/test-metapipeline-DNA-fastq-input/input.yaml +++ b/test/test-metapipeline-DNA-fastq-input/input.yaml @@ -1,39 +1,39 @@ --- input: FASTQ: - - patient: "BZPRGPT1000001" - sample: "BZPRGPT1000001-N001-B01-F" - state: "normal" - read_group_identifier: "FD00122592.1.SeqL001" - sequencing_center: "FD00122592" - library_identifier: "FD00122592" - platform_technology: "ILLUMINA" - platform_unit: "HKTWMDRXY.1" - bam_header_sm: "BZPRGPT1000001-N001-B01-F" - lane: 0 - read1_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/BZPRGPT1000001-N001-B01-F/FD00122592.1.SeqL001_collated_R1.fq.gz" - read2_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/BZPRGPT1000001-N001-B01-F/FD00122592.1.SeqL001_collated_R2.fq.gz" - - patient: "BZPRGPT1000001" - sample: "BZPRGPT1000002-N001-B01-F" + - patient: "IlluminaPatient1" + sample: "NA24143" state: "tumor" - read_group_identifier: "FD00123067.1.SeqL001" - sequencing_center: "FD00123067" - library_identifier: "FD00123067" - platform_technology: "ILLUMINA" - platform_unit: "HKTWMDRXY.1" - bam_header_sm: "BZPRGPT1000002-N001-B01-F" - lane: 0 - read1_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/BZPRGPT1000002-N001-B01-F/FD00123067.1.SeqL001_collated_R1.fq.gz" - read2_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/BZPRGPT1000002-N001-B01-F/FD00123067.1.SeqL001_collated_R2.fq.gz" - - patient: "BZPRGPT1000001" - sample: "BZPRGPT1000003-N001-B01-F" + read_group_identifier: "NA24143RG" + sequencing_center: "Illumina" + library_identifier: "NA24143LIB" + platform_technology: "Illumina" + platform_unit: "Platform1" + bam_header_sm: "NA24143" + lane: 1 + read1_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24143/IDPE2plus-NA24143-R4-MitoEx-1to100_S21_L001_R1_001.fastq.gz" + read2_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24143/IDPE2plus-NA24143-R4-MitoEx-1to100_S21_L001_R2_001.fastq.gz" + - patient: "IlluminaPatient1" + sample: "NA24149" + state: "normal" + read_group_identifier: "NA24149RG" + sequencing_center: "Illumina" + library_identifier: "NA24149LIB" + platform_technology: "Illumina" + platform_unit: "Platform1" + bam_header_sm: "NA24149" + lane: 1 + read1_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24149/IDPE2plus-NA24149-R3-MitoEx-1to1000_S41_L001_R1_001.fastq.gz" + read2_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24149/IDPE2plus-NA24149-R3-MitoEx-1to1000_S41_L001_R2_001.fastq.gz" + - patient: "IlluminaPatient1" + sample: "NA24385" state: "tumor" - read_group_identifier: "FD00123289.1.SeqL001" - sequencing_center: "FD00123289" - library_identifier: "FD00123289" - platform_technology: "ILLUMINA" - platform_unit: "HKTWMDRXY.1" - bam_header_sm: "BZPRGPT1000003-N001-B01-F" - lane: 0 - read1_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/BZPRGPT1000003-N001-B01-F/FD00123289.1.SeqL001_collated_R1.fq.gz" - read2_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/BZPRGPT1000003-N001-B01-F/FD00123289.1.SeqL001_collated_R2.fq.gz" + read_group_identifier: "NA24385RG" + sequencing_center: "Illumina" + library_identifier: "NA24385LIB" + platform_technology: "Illumina" + platform_unit: "Platform1" + bam_header_sm: "NA24385" + lane: 1 + read1_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24385/IDPE2plus-NA24385-R2-MitoEx-1to10_S56_L001_R1_001.fastq.gz" + read2_fastq: "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24385/IDPE2plus-NA24385-R2-MitoEx-1to10_S56_L001_R2_001.fastq.gz" diff --git a/test/test-metapipeline-DNA-fastq-input/test.config b/test/test-metapipeline-DNA-fastq-input/test.config index 8231ccff..af4c38a2 100644 --- a/test/test-metapipeline-DNA-fastq-input/test.config +++ b/test/test-metapipeline-DNA-fastq-input/test.config @@ -3,10 +3,9 @@ includeConfig "${projectDir}/config/methods.config" includeConfig "${projectDir}/nextflow.config" params { - // leading_work_dir = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/common_work_dir' - leading_work_dir = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-save-files-and-logs/work' + leading_work_dir = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/common_work_dir' pipeline_work_dir = '/scratch' //For individual pipeline outputs before copying to output_dir - project_id = 'BZPRGPT1' + project_id = 'IlluminaTest' save_intermediate_files = true partition = 'F32' clusterOptions = '--exclusive' @@ -83,6 +82,7 @@ params { reference_fasta = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' exclusion_file = '/hot/ref/tool-specific-input/Delly/GRCh38/human.hg38.excl.tsv' mappability_map = '/hot/ref/tool-specific-input/Delly/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz' + run_delly = false } call_sSV { algorithm = ['delly', 'manta'] diff --git a/test/test-metapipeline-DNA/input.csv b/test/test-metapipeline-DNA/input.csv index ec19140d..6df0d796 100644 --- a/test/test-metapipeline-DNA/input.csv +++ b/test/test-metapipeline-DNA/input.csv @@ -1,3 +1,3 @@ patient,sample,state,bam -BZPRGPT1000001,BZPRGPT1000001-N001-B01-F,normal,/hot/data/unregistered/Boutros-Zeltser-PRAD-GPT1/align-DNA/align-DNA-BZPRGPT1000001-N001-B01-F/align-DNA-20211213-144945/BWA-MEM2-2.2.1/BZPRGPT1000001-N001-B01-F.bam -BZPRGPT1000001,BZPRGPT1000002-N001-B01-F,tumor,/hot/data/unregistered/Boutros-Zeltser-PRAD-GPT1/align-DNA/align-DNA-BZPRGPT1000002-N001-B01-F/align-DNA-20211213-153513/BWA-MEM2-2.2.1/BZPRGPT1000002-N001-B01-F.bam +IlluminaPatient1,NA24143,tumor,/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24143.bam +IlluminaPatient1,NA24149,normal,/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24149.bam diff --git a/test/test-metapipeline-DNA/pipeline_specific_params.json b/test/test-metapipeline-DNA/pipeline_specific_params.json index 1deb6c0a..a43b3ac0 100644 --- a/test/test-metapipeline-DNA/pipeline_specific_params.json +++ b/test/test-metapipeline-DNA/pipeline_specific_params.json @@ -143,12 +143,14 @@ "reference_fasta": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", "exclusion_file": "/hot/ref/tool-specific-input/Delly/GRCh38/human.hg38.excl.tsv", "mappability_map": "/hot/ref/tool-specific-input/Delly/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz", + "run_delly": false, "is_pipeline_enabled": true, "subworkflow_cpus": 8, "metapipeline_arg_map": { "reference_fasta": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", "exclusion_file": "/hot/ref/tool-specific-input/Delly/GRCh38/human.hg38.excl.tsv", "mappability_map": "/hot/ref/tool-specific-input/Delly/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz", + "run_delly": false, "is_pipeline_enabled": true, "subworkflow_cpus": 8 } @@ -198,7 +200,7 @@ } }, "sample_data": { - "BZPRGPT1000001-N001-B01-F": { + "NA24149": { "align-DNA": { "BWA-MEM2": { "BAM": "" @@ -212,12 +214,12 @@ ], "original_data": { - "path": "/hot/data/unregistered/Boutros-Zeltser-PRAD-GPT1/align-DNA/align-DNA-BZPRGPT1000001-N001-B01-F/align-DNA-20211213-144945/BWA-MEM2-2.2.1/BZPRGPT1000001-N001-B01-F.bam" + "path": "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24149.bam" }, - "patient": "BZPRGPT1000001", + "patient": "IlluminaPatient1", "state": "normal" }, - "BZPRGPT1000002-N001-B01-F": { + "NA24143": { "align-DNA": { "BWA-MEM2": { "BAM": "" @@ -231,9 +233,9 @@ ], "original_data": { - "path": "/hot/data/unregistered/Boutros-Zeltser-PRAD-GPT1/align-DNA/align-DNA-BZPRGPT1000002-N001-B01-F/align-DNA-20211213-153513/BWA-MEM2-2.2.1/BZPRGPT1000002-N001-B01-F.bam" + "path": "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24143.bam" }, - "patient": "BZPRGPT1000001", + "patient": "IlluminaPatient1", "state": "tumor" } }, diff --git a/test/test-metapipeline-DNA/test.config b/test/test-metapipeline-DNA/test.config index 382fac2d..ed8d5a1b 100644 --- a/test/test-metapipeline-DNA/test.config +++ b/test/test-metapipeline-DNA/test.config @@ -4,10 +4,10 @@ params { input_csv = "${projectDir}/../test/test-metapipeline-DNA/input.csv" leading_work_dir = "/hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/common_work_dir" work_dir = '/scratch/\$SLURM_JOB_ID' //For individual pipeline outputs before copying to output_dir - project_id = 'LUAD0000034' + project_id = 'IlluminaTest' save_intermediate_files = true - patient = "BZPRGPT1000001" + patient = "IlluminaPatient1" partition = 'F32' clusterOptions = '--exclusive' diff --git a/test/test-recalibrate-BAM/test.config b/test/test-recalibrate-BAM/test.config index f7b5e64e..8232b3d0 100644 --- a/test/test-recalibrate-BAM/test.config +++ b/test/test-recalibrate-BAM/test.config @@ -3,8 +3,8 @@ import nextflow.util.SysHelper params { work_dir = '/scratch/\$SLURM_JOB_ID' save_intermediate_files = true - patient = 'TCEB1' - project_id = 'test' + patient = 'IlluminaPatient1' + project_id = 'IlluminaTest' sample_mode = 'single' override_recalibrate_bam = false @@ -35,16 +35,16 @@ params { params.metapipeline_log_output_dir = "${params.output_dir}/log-test-recalibrate-BAM" params.sample_data = [ - 'S00-9422T-027-166': [ - 'patient': 'TCEB1_RCC_S00', + 'NA24143': [ + 'patient': 'IlluminaPatient1', 'state': 'tumor', - 'align-DNA': ['BWA-MEM2': ['BAM': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/inputs/TCEB1/TCEB1_RCC_S00-9422T-027-166.bam']], + 'align-DNA': ['BWA-MEM2': ['BAM': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24143.bam']], 'recalibrate-BAM': ['BAM':'', 'contamination_table':''] ], - 'S00-9422N-079-114': [ - 'patient': 'TCEB1_RCC_S00', + 'NA24149': [ + 'patient': 'IlluminaPatient1', 'state': 'normal', - 'align-DNA': ['BWA-MEM2': ['BAM': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/inputs/TCEB1/TCEB1_RCC_S00-9422N-079-114.bam']], + 'align-DNA': ['BWA-MEM2': ['BAM': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24149.bam']], 'recalibrate-BAM': ['BAM':'', 'contamination_table':''] ] ]