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Standaridse parameters

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This commit is contained in:
James Fellows Yates 2022-06-02 20:27:16 +02:00
parent 7ffe98ac8b
commit 599b264280
1 changed files with 14 additions and 4 deletions
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18
modules/gatk/indelrealigner/main.nf
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@ -8,9 +8,11 @@ process GATK_INDELREALIGNER {
'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), path(intervals) tuple val(meta), path(input), path(index), path(intervals)
tuple val(meta), path(fasta) path path(fasta)
tuple val(meta), path(known_vcf) path(fai)
path(dict)
path(known_vcf)
output: output:
tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.bam"), emit: bam
@ -24,9 +26,17 @@ process GATK_INDELREALIGNER {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def known = known_vcf ? "-known ${known_vcf}" : "" def known = known_vcf ? "-known ${known_vcf}" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[GATK IndelRealigner] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
""" """
gatk3 \\ gatk3 \\
-T RealignerTargetCreator \\ -T IndelRealigner \\
-R ${fasta} \\ -R ${fasta} \\
-nt ${task.cpus} -nt ${task.cpus}
-I ${bam} \\ -I ${bam} \\