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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: gsv_discovery-all-tools-std-input
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-*/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-*/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-*/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-*/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-*/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
message: test development branch using Manta and an a-mini standard paired tumor and normal input
nf_script: ./main.nf
nf_config: ./test/config/gsv_discovery-manta.config
params_file: ./test/yaml/gsv-manta-input-a-mini.yaml
skip: false
verbose: true
asserts:
- actual: call-gSV-*/HG002.N/Manta-*/output/Manta-*_TEST_HG002.N_candidateSmallIndels.vcf.gz
expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-manta-std-input/HG002.N/Manta-1.6.0/Manta-1.6.0_TEST_HG002.N_candidateSmallIndels.vcf.gz
script: test/assert_bcf_vcf.sh
- actual: call-gSV-*/HG002.N/Manta-*/output/Manta-*_TEST_HG002.N_candidateSV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-manta-std-input/HG002.N/Manta-1.6.0/Manta-1.6.0_TEST_HG002.N_candidateSV.vcf.gz
script: test/assert_bcf_vcf.sh
- actual: call-gSV-*/HG002.N/Manta-*/output/Manta-*_TEST_HG002.N_diploidSV.vcf.gz
expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-manta-std-input/HG002.N/Manta-1.6.0/Manta-1.6.0_TEST_HG002.N_diploidSV.vcf.gz
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 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-*/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-*/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