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Update for mutect2: add output channel for stats file (#716)

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* added output channel for stats file, updated meta yml with description and test yml with check for stats file

* Update modules/gatk4/mutect2/main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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GCJMackenzie 2021-09-17 09:56:56 +01:00 committed by GitHub
parent 7e45cbf4d1
commit 3c4eaec52b
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3 changed files with 14 additions and 3 deletions
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7
modules/gatk4/mutect2/main.nf
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@ -31,10 +31,11 @@ process GATK4_MUTECT2 {
path panel_of_normals_idx path panel_of_normals_idx
output: output:
tuple val(meta), path("*.vcf.gz"), emit: vcf tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi tuple val(meta), path("*.tbi") , emit: tbi
tuple val(meta), path("*.stats") , emit: stats
tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2 tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)

4
modules/gatk4/mutect2/meta.yml
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@ -76,6 +76,10 @@ output:
type: file type: file
description: Index of vcf file description: Index of vcf file
pattern: "*vcf.gz.tbi" pattern: "*vcf.gz.tbi"
- stats:
type: file
description: Stats file that pairs with output vcf file
pattern: "*vcf.gz.stats"
- f1r2: - f1r2:
type: file type: file
description: file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run) description: file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)

6
tests/modules/gatk4/mutect2/test.yml
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@ -6,6 +6,8 @@
files: files:
- path: output/gatk4/test.f1r2.tar.gz - 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
md5sum: 6ecb874e6a95aa48233587b876c2a7a9
- path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single - name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
@ -15,6 +17,8 @@
- gatk4/mutect2 - gatk4/mutect2
files: files:
- path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz
- path: output/gatk4/test.vcf.gz.stats
md5sum: e7ef613f7d158b8a0adf44abe5db2029
- path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 mutect2 test_gatk4_mutect2_generate_pon - name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
@ -24,4 +28,6 @@
- gatk4/mutect2 - gatk4/mutect2
files: files:
- path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz
- path: output/gatk4/test.vcf.gz.stats
md5sum: 4f77301a125913170b8e9e7828b4ca3f
- path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/test.vcf.gz.tbi