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remove variables used for test data generation, add tbi

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Rike 2022-05-22 13:34:56 +02:00
parent 520dd06ca3
commit 5d72500d60
4 changed files with 21 additions and 7 deletions
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9
modules/gatk4/cnnscorevariants/main.nf
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@ -9,7 +9,7 @@ process GATK4_CNNSCOREVARIANTS {
container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package
input:
tuple val(meta), path(vcf), path(aligned_input), path(intervals)
tuple val(meta), path(vcf), path(tbi), path(aligned_input), path(intervals)
path fasta
path fai
path dict
@ -17,8 +17,9 @@ process GATK4_CNNSCOREVARIANTS {
path weights
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions
tuple val(meta), path("*cnn.vcf.gz") , emit: vcf
tuple val(meta), path("*cnn.vcf.gz.tbi"), emit: tbi
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -40,7 +41,7 @@ process GATK4_CNNSCOREVARIANTS {
"""
gatk --java-options "-Xmx${avail_mem}g" CNNScoreVariants \\
--variant $vcf \\
--output ${prefix}.vcf.gz \\
--output ${prefix}.cnn.vcf.gz \\
--reference $fasta \\
$interval_command \\
$aligned_input \\

8
modules/gatk4/cnnscorevariants/meta.yml
View file

@ -25,6 +25,10 @@ input:
type: file
description: VCF file
pattern: "*.vcf.gz"
- tbi:
type: file
description: VCF index file
pattern: "*.vcf.gz.tbi"
- aligned_input:
type: file
description: BAM/CRAM file from alignment (optional)
@ -67,6 +71,10 @@ output:
type: file
description: Annotated VCF file
pattern: "*.vcf"
- tbi:
type: file
description: VCF index file
pattern: "*.vcf.gz.tbi"
authors:
- "@FriederikeHanssen"

7
modules/gatk4/filtervarianttranches/main.nf
View file

@ -8,7 +8,7 @@ process GATK4_FILTERVARIANTTRANCHES {
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(tbi),path(intervals)
tuple val(meta), path(vcf), path(tbi), path(intervals)
path resources
path resources_index
path fasta
@ -17,8 +17,9 @@ process GATK4_FILTERVARIANTTRANCHES {
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions
tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when

4
modules/gatk4/filtervarianttranches/meta.yml
View file

@ -59,6 +59,10 @@ output:
type: file
description: VCF file
pattern: "*.vcf.gz"
- tbi:
type: file
description: VCF index file
pattern: "*.vcf.gz.tbi"
authors:
- "@FriederikeHanssen"