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nf-core_modules/tests/modules/gatk4/genotypegvcfs/test.yml

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- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_vcf_input
command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains:
[
"AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input
command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains:
[
"AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp
command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains:
[
"AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_intervals
command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains:
[
"AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals
command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains: ["AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693"]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains:
[
"AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp
command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains:
[
"AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_intervals
command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains:
[
"AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals
command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains: ["AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693"]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
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