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nftest.yml
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nftest.yml
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---
global:
temp_dir: ./test/work
nf_config: test/global.config
remove_temp: false
clean_logs: true
cases:
- 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
asserts:
- actual: call-sSNV-*/S2-v1.1.5/MuSE-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/MuSE-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/SomaticSniper-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-1-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-2-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_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-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_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-*/TWGSAMIN000001/Mutect2-*/output/Mutect2-*_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/TWGSAMIN000001/Mutect2-*/output/Mutect2-*_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/TWGSAMIN000001/Mutect2-*/output/Mutect2-*_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/Mutect2-4.6.1.0_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz
script: test/assert_vcf.sh
- name: a_mini-two-tools
message: test development branch using somaticsniper and strelka2 with standard paired tumor and normal a-mini-n2 input
nf_script: ./main.nf
nf_config: ./test/config/a_mini-two-tools.config
params_file: ./test/yaml/a_mini_n2-std-input.yaml
skip: false
verbose: true
asserts:
- actual: call-sSNV-*/S2-v1.1.5/SomaticSniper-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-1-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-2-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.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-*/S2-v1.1.5/SomaticSniper-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_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-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Strelka2-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_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-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_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-*/S2-v1.1.5/MuSE-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
script: test/assert_vcf.sh
- name: a_mini-all-tools-vcf-input
message: test development branch a-mini four VCFs input
nf_script: ./main.nf
nf_config: ./test/config/a_mini-all-tools.config
params_file: ./test/yaml/a_mini-vcf.yaml
skip: true
verbose: true
asserts:
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-1-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-2-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
method: md5
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/MuSE-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/MuSE-2.0.3_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
script: test/assert_vcf.sh
- actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
script: test/assert_vcf.sh