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fix gatk4_mutect2 test

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This commit is contained in:
Lucpen 2022-05-02 14:16:07 +02:00
parent 3a4e415fe2
commit da82e06354
2 changed files with 12 additions and 7 deletions
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14
tests/modules/gatk4/mutect2/main.nf
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@ -119,10 +119,14 @@ workflow test_gatk4_mutect2_mitochondria {
GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] ) GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] )
} }
workflow test_gatk4_mutect2_tumor_single_stubs { workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
input = [ [ id:'test'], // meta map input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
[ "foo.bam" ], [ "foo_parired.bam",
[ "foo.bam.bai" ], "foo_parired2.bam"
],
[ "foo_parired.bam.bai",
"foo_parired2.bam.bai"
],
[] []
] ]
@ -134,5 +138,5 @@ workflow test_gatk4_mutect2_tumor_single_stubs {
panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz" panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi" panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
} }

5
tests/modules/gatk4/mutect2/test.yml
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@ -70,12 +70,13 @@
- path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/test.vcf.gz.tbi
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single_stubs - name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
tags: tags:
- gatk4 - gatk4
- gatk4/mutect2 - gatk4/mutect2
files: files:
- path: output/gatk4/test.f1r2.tar.gz
- path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz
- path: output/gatk4/test.vcf.gz.stats - path: output/gatk4/test.vcf.gz.stats
- path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/test.vcf.gz.tbi