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This commit is contained in:
James Fellows Yates 2022-06-02 20:24:14 +02:00
parent 7633d7816b
commit 14c63f9ccc
2 changed files with 15 additions and 5 deletions
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14
modules/gatk/realignertargetcreator/main.nf
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@ -8,8 +8,10 @@ process GATK_REALIGNERTARGETCREATOR {
'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }" 'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(input), path(index)
tuple path(fasta), path(fasta_fai), path(fasta_dict) path path(fasta)
path(fai)
path(dict)
path(known_vcf) path(known_vcf)
output: output:
@ -25,8 +27,16 @@ process GATK_REALIGNERTARGETCREATOR {
def known = known_vcf ? "-known ${known_vcf}" : "" def known = known_vcf ? "-known ${known_vcf}" : ""
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
def avail_mem = 3
if (!task.memory) {
log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
""" """
gatk3 \\ gatk3 \\
-Xmx${avail_mem}g \\
-T RealignerTargetCreator \\ -T RealignerTargetCreator \\
-nt ${task.cpus} \\ -nt ${task.cpus} \\
-I ${bam} \\ -I ${bam} \\

6
modules/gatk/realignertargetcreator/meta.yml
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@ -20,11 +20,11 @@ input:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- bam: - input:
type: file type: file
description: Sorted and indexed BAM/CRAM/SAM file description: Sorted and indexed BAM/CRAM/SAM file
pattern: "*.bam" pattern: "*.bam"
- bai: - index:
type: file type: file
description: BAM index file description: BAM index file
pattern: "*.bai" pattern: "*.bai"
@ -32,7 +32,7 @@ input:
type: file type: file
description: Reference file used to generate BAM file description: Reference file used to generate BAM file
pattern: ".{fasta,fa,fna}" pattern: ".{fasta,fa,fna}"
- fasta_fai: - fai:
type: file type: file
description: Index of reference file used to generate BAM file description: Index of reference file used to generate BAM file
pattern: ".fai" pattern: ".fai"