From 1cf467fb660bb3cff75ed58c84187862fe61a690 Mon Sep 17 00:00:00 2001 From: Mohammed Faizal Eeman Mootor <68152431+Faizal-Eeman@users.noreply.github.com> Date: Thu, 2 May 2024 14:15:36 -0700 Subject: [PATCH] Update NFTest sample (#144) * replace CPCG with HG003 as NFtest sample * replace CPCG with HG003 * Update CHANGELOG.md * Autofix Nextflow configuration regression tests --------- Co-authored-by: Mootor Co-authored-by: nwiltsie --- CHANGELOG.md | 1 + nftest.yaml | 32 +++++++++++++++---------------- test/configtest-F16.json | 4 ++-- test/yaml/gsv_test-std-input.yaml | 2 +- 4 files changed, 20 insertions(+), 19 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8468ee6d..3f9c6cd5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ All notable changes to the call-gSV pipeline. ## [Unreleased] ### Changed +- Use HG003 as test sample for NFTest - Update Nextflow configuration test workflows --- diff --git a/nftest.yaml b/nftest.yaml index f58c569d..e74c1dc7 100644 --- a/nftest.yaml +++ b/nftest.yaml @@ -7,31 +7,31 @@ global: cases: - name: gsv_discovery-all-tools-std-input - message: test development branch using all tools and standard paired tumor and normal test input CPCG0196-B1 of a-partial size + message: test development branch using all tools and standard paired tumor and normal test input HG003 of 5X depth of coverage nf_script: ./main.nf nf_config: ./test/config/gsv_discovery-all-tools.config params_file: ./test/yaml/gsv_test-std-input.yaml skip: false verbose: true asserts: - - actual: call-gSV-*/CPCG0196-B1/DELLY-*/output/DELLY-*_TEST_CPCG0196-B1_gCNV.bcf - expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/DELLY-1.2.6/DELLY-1.2.6_TEST_CPCG0196-B1_gCNV.bcf + - actual: call-gSV-*/HG003/DELLY-*/output/DELLY-*_TEST_HG003_gCNV.bcf + expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/DELLY-1.2.6/DELLY-1.2.6_TEST_HG003_gCNV.bcf script: test/assert_bcf_vcf.sh - - actual: call-gSV-*/CPCG0196-B1/DELLY-*/output/DELLY-*_TEST_CPCG0196-B1_gSV.bcf - expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/DELLY-1.2.6/DELLY-1.2.6_TEST_CPCG0196-B1_gSV.bcf + - actual: call-gSV-*/HG003/DELLY-*/output/DELLY-*_TEST_HG003_gSV.bcf + expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/DELLY-1.2.6/DELLY-1.2.6_TEST_HG003_gSV.bcf script: test/assert_bcf_vcf.sh - - actual: call-gSV-*/CPCG0196-B1/Manta-*/output/Manta-*_TEST_CPCG0196-B1_candidateSmallIndels.vcf.gz - expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/Manta-1.6.0/Manta-1.6.0_TEST_CPCG0196-B1_candidateSmallIndels.vcf.gz + - actual: call-gSV-*/HG003/Manta-*/output/Manta-*_TEST_HG003_candidateSmallIndels.vcf.gz + expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/Manta-1.6.0/Manta-1.6.0_TEST_HG003_candidateSmallIndels.vcf.gz script: test/assert_bcf_vcf.sh - - actual: call-gSV-*/CPCG0196-B1/Manta-*/output/Manta-*_TEST_CPCG0196-B1_candidateSV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/Manta-1.6.0/Manta-1.6.0_TEST_CPCG0196-B1_candidateSV.vcf.gz + - actual: call-gSV-*/HG003/Manta-*/output/Manta-*_TEST_HG003_candidateSV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/Manta-1.6.0/Manta-1.6.0_TEST_HG003_candidateSV.vcf.gz script: test/assert_bcf_vcf.sh - - actual: call-gSV-*/CPCG0196-B1/Manta-*/output/Manta-*_TEST_CPCG0196-B1_diploidSV.vcf.gz - expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/Manta-1.6.0/Manta-1.6.0_TEST_CPCG0196-B1_diploidSV.vcf.gz + - actual: call-gSV-*/HG003/Manta-*/output/Manta-*_TEST_HG003_diploidSV.vcf.gz + expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/Manta-1.6.0/Manta-1.6.0_TEST_HG003_diploidSV.vcf.gz script: test/assert_bcf_vcf.sh - name: gsv_discovery-manta-std-input @@ -55,17 +55,17 @@ cases: script: test/assert_bcf_vcf.sh - name: gsv_discovery-delly-std-input - message: test development branch using DELLY and a standard paired tumor and normal test input CPCG0196-B1 of a-partial size + message: test development branch using DELLY and a standard paired tumor and normal test input HG003 of a-partial size nf_script: ./main.nf nf_config: ./test/config/gsv_discovery-delly.config params_file: ./test/yaml/gsv_test-std-input.yaml skip: false verbose: true asserts: - - actual: call-gSV-*/CPCG0196-B1/DELLY-*/output/DELLY-*_TEST_CPCG0196-B1_gCNV.bcf - expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/DELLY-1.2.6/DELLY-1.2.6_TEST_CPCG0196-B1_gCNV.bcf + - actual: call-gSV-*/HG003/DELLY-*/output/DELLY-*_TEST_HG003_gCNV.bcf + expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/DELLY-1.2.6/DELLY-1.2.6_TEST_HG003_gCNV.bcf script: test/assert_bcf_vcf.sh - - actual: call-gSV-*/CPCG0196-B1/DELLY-*/output/DELLY-*_TEST_CPCG0196-B1_gSV.bcf - expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/DELLY-1.2.6/DELLY-1.2.6_TEST_CPCG0196-B1_gSV.bcf + - actual: call-gSV-*/HG003/DELLY-*/output/DELLY-*_TEST_HG003_gSV.bcf + expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/DELLY-1.2.6/DELLY-1.2.6_TEST_HG003_gSV.bcf script: test/assert_bcf_vcf.sh diff --git a/test/configtest-F16.json b/test/configtest-F16.json index 530db852..8f80cc8f 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -66,7 +66,7 @@ "input": { "BAM": { "normal": [ - "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/CPCG0196-B1-downsampled-a-partial-sorted.bam" + "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/BWA-MEM2-2.2.1_GATK-4.2.4.1_0000082_HG003_subsampled_5X_sorted.bam" ] } }, @@ -191,7 +191,7 @@ "sample_to_process": [ { "id": "8675309", - "path": "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/CPCG0196-B1-downsampled-a-partial-sorted.bam", + "path": "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/BWA-MEM2-2.2.1_GATK-4.2.4.1_0000082_HG003_subsampled_5X_sorted.bam", "sample_type": "normal" } ], diff --git a/test/yaml/gsv_test-std-input.yaml b/test/yaml/gsv_test-std-input.yaml index 1009be31..f4bc7f4e 100644 --- a/test/yaml/gsv_test-std-input.yaml +++ b/test/yaml/gsv_test-std-input.yaml @@ -2,4 +2,4 @@ input: BAM: normal: - - "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/CPCG0196-B1-downsampled-a-partial-sorted.bam" + - "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/BWA-MEM2-2.2.1_GATK-4.2.4.1_0000082_HG003_subsampled_5X_sorted.bam"