Changes after review

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

View file

@ -8,8 +8,10 @@ process GATK_REALIGNERTARGETCREATOR {
'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
input:
tuple val(meta), path(bam), path(bai)
tuple path(fasta), path(fasta_fai), path(fasta_dict)
tuple val(meta), path(input), path(index)
path path(fasta)
path(fai)
path(dict)
path(known_vcf)
output:
@ -25,8 +27,16 @@ process GATK_REALIGNERTARGETCREATOR {
def known = known_vcf ? "-known ${known_vcf}" : ""
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
def avail_mem = 3
if (!task.memory) {
log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk3 \\
-Xmx${avail_mem}g \\
-T RealignerTargetCreator \\
-nt ${task.cpus} \\
-I ${bam} \\

View file

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