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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: true
clean_logs: true
cases:
- name: test-call-gSNP-paired
message: Test call-gSNP pipeline with one normal and one tumor pair
nf_script: ./main.nf
nf_config: test/test-call-gSNP-paired.config
params_file: test/Illumina-paired.yaml
skip: false
verbose: true
asserts:
- actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143.g.vcf.gz
expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143.g.vcf.gz
script: test/assert-vcf.sh
- actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143_indel.vcf.gz
expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143_indel.vcf.gz
script: test/assert-vcf.sh
- actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143_snv.vcf.gz
expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143_snv.vcf.gz
script: test/assert-vcf.sh
- actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143.vcf.gz
expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143.vcf.gz
script: test/assert-vcf.sh
- actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143_VQSR-SNP-AND-INDEL.vcf.gz
expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143_VQSR-SNP-AND-INDEL.vcf.gz
script: test/assert-vcf.sh
- actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24149.g.vcf.gz
expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24149.g.vcf.gz
script: test/assert-vcf.sh
- actual: call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143_genotype-count.tsv
expect: /hot/software/pipeline/pipeline-call-gSNP/Nextflow/development/output/test-call-gSNP-paired/call-gSNP-10.1.0-rc.1/NA24143/GATK-4.5.0.0/output/GATK-4.5.0.0_IlluminaTest_NA24143_genotype-count.tsv
method: md5