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Merge branch 'sfitz-nftest-assertions' of github.com:uclahs-cds/pipel…
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…ine-call-sSNV into sfitz-vcf-sample-orders
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@sorelfitzgibbon
sorelfitzgibbon committed Sep 29, 2023
2 parents e6c037a + c1b4f46 commit 81728fc
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Update plot-venn.R to work with all numbers of algorithms greater than two

### Added
- Add assertions to `nftest`
- Add compression of `SomaticSniper` `bam-readcount` output and move to `intermediate` directory
- Add `ncbi_build` parameter
- Add conversion of concatenated VCF to MAF
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138 changes: 136 additions & 2 deletions nftest.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,52 +6,186 @@ global:
clean_logs: true

cases:
- name: a_mini_n2-all-tools-std-input
- name: a_mini-all-tools-std-input
message: test development branch using all tools and standard paired tumor and normal a-mini-n2 input
nf_script: ./main.nf
nf_config: ./test/config/a_mini-all-tools.config
params_file: ./test/yaml/a_mini_n2-std-input.yaml
skip: false
verbose: true
- name: a_mini_n2-mutect2-tumor-only
asserts:
- actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/MuSE-2.0.2/output/MuSE-2.0.2_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-2.0.2/MuSE-2.0.2_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
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
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
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-2.0.2/output/MuSE-2.0.2_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-2.0.2/MuSE-2.0.2_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
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
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
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
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
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
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
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
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
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
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-2.0.2_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-2.0.2_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
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
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
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

- name: a_mini-mutect2-tumor-only
message: test development branch using mutect2 and only a single tumor a-mini-n2 input
nf_script: ./main.nf
nf_config: ./test/config/a_mini-mutect2.config
params_file: ./test/yaml/a_mini_n2-tumor-only.yaml
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
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
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
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

- name: a_mini-mutect2-multiple-samples
message: test development branch using mutect2, a-mini-n1 and a-mini-n2 input and a single matched normal
nf_script: ./main.nf
nf_config: ./test/config/a_mini-mutect2.config
params_file: ./test/yaml/a_mini-multiple-samples.yaml
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
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
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
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

- name: a_mini-somaticsniper
message: test development branch using somaticsniper and standard paired tumor and normal a-mini-n2 input
nf_script: ./main.nf
nf_config: ./test/config/a_mini-somaticsniper.config
params_file: ./test/yaml/a_mini_n2-std-input.yaml
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
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

- name: a_mini-strelka2
message: test development branch using strelka2 and standard paired tumor and normal a-mini-n2 input
nf_script: ./main.nf
nf_config: ./test/config/a_mini-strelka2.config
params_file: ./test/yaml/a_mini_n2-std-input.yaml
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
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
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

- name: a_mini-mutect2
message: test development branch using mutect2 and standard paired tumor and normal a-mini-n2 input
nf_script: ./main.nf
nf_config: ./test/config/a_mini-mutect2.config
params_file: ./test/yaml/a_mini_n2-std-input.yaml
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
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
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
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

- name: a_mini-muse
message: test development branch using muse and standard paired tumor and normal a-mini-n2 input
nf_script: ./main.nf
nf_config: ./test/config/a_mini-muse.config
params_file: ./test/yaml/a_mini_n2-std-input.yaml
skip: true
verbose: true
asserts:
- actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/MuSE-2.0.2/output/MuSE-2.0.2_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-2.0.2/MuSE-2.0.2_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz
script: test/assert_vcf.sh
15 changes: 15 additions & 0 deletions test/assert_vcf.sh
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
#!/bin/bash
function md5_vcf {
zcat $1 | grep -v '^##' | md5sum | cut -f 1 -d ' '
}

received=$(md5_vcf $1)
expected=$(md5_vcf $2)

if [ "$received" == "$expected" ]; then
echo "VCF files are equal"
exit 0
else
echo "VCF files are not equal" >&2
exit 1
fi

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