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nftest.yaml
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nftest.yaml
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---
global:
temp_dir: ./test/work
nf_config: test/global.config
remove_temp: true
clean_logs: true
cases:
- name: ssv-all-tools-std-input
message: test development branch using all tools and standard paired tumor and normal a-mini input
nf_script: ./main.nf
nf_config: ./test/config/ssv-all-tools.config
params_file: ./test/yaml/ssv_test-std-input.yaml
skip: false
verbose: true
asserts:
- actual: call-sSV-*/S2_v1.1.5/DELLY-1.2.6/output/DELLY-1.2.6_TWGSAMIN000001_S2-v1.1.5.bcf
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/DELLY-1.2.6/DELLY-1.2.6_TWGSAMIN000001_S2-v1.1.5.bcf
script: test/assert_bcf_vcf.sh
- actual: call-sSV-*/S2_v1.1.5/Manta-1.6.0/output/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_candidateSmallIndels.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/Manta-1.6.0/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_candidateSmallIndels.vcf.gz
script: test/assert_bcf_vcf.sh
- actual: call-sSV-*/S2_v1.1.5/Manta-1.6.0/output/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_candidateSV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/Manta-1.6.0/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_candidateSV.vcf.gz
script: test/assert_bcf_vcf.sh
- actual: call-sSV-*/S2_v1.1.5/Manta-1.6.0/output/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_diploidSV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/Manta-1.6.0/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_diploidSV.vcf.gz
script: test/assert_bcf_vcf.sh
- actual: call-sSV-*/S2_v1.1.5/Manta-1.6.0/output/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_somaticSV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/Manta-1.6.0/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_somaticSV.vcf.gz
script: test/assert_bcf_vcf.sh
- name: ssv-delly-std-input
message: test development branch using DELLY and standard paired tumor and normal a-mini input
nf_script: ./main.nf
nf_config: ./test/config/ssv-delly.config
params_file: ./test/yaml/ssv_test-std-input.yaml
skip: false
verbose: true
asserts:
- actual: call-sSV-*/S2_v1.1.5/DELLY-1.2.6/output/DELLY-1.2.6_TWGSAMIN000001_S2-v1.1.5.bcf
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/DELLY-1.2.6/DELLY-1.2.6_TWGSAMIN000001_S2-v1.1.5.bcf
script: test/assert_bcf_vcf.sh
- name: ssv-manta-std-input
message: test development branch using Manta and standard paired tumor and normal a-mini input
nf_script: ./main.nf
nf_config: ./test/config/ssv-manta.config
params_file: ./test/yaml/ssv_test-std-input.yaml
skip: false
verbose: true
asserts:
- actual: call-sSV-*/S2_v1.1.5/Manta-1.6.0/output/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_candidateSmallIndels.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/Manta-1.6.0/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_candidateSmallIndels.vcf.gz
script: test/assert_bcf_vcf.sh
- actual: call-sSV-*/S2_v1.1.5/Manta-1.6.0/output/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_candidateSV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/Manta-1.6.0/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_candidateSV.vcf.gz
script: test/assert_bcf_vcf.sh
- actual: call-sSV-*/S2_v1.1.5/Manta-1.6.0/output/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_diploidSV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/Manta-1.6.0/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_diploidSV.vcf.gz
script: test/assert_bcf_vcf.sh
- actual: call-sSV-*/S2_v1.1.5/Manta-1.6.0/output/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_somaticSV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/test-output/ssv-all-tools-std-input/S2-v1.1.5/Manta-1.6.0/Manta-1.6.0_TWGSAMIN000001_S2-v1.1.5_somaticSV.vcf.gz
script: test/assert_bcf_vcf.sh