haplotyper-battle-royale/modules/cliquesnv/main.nf

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process CLIQUESNV {
tag "${prefix}"
label 'process_high'
label 'cliquesnv'
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container 'quay.io/biocontainers/cliquesnv:2.0.3--hdfd78af_0'
input:
tuple val(prefix), path(bam), path(bai)
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val(method)
output:
tuple val(prefix), path("*.json")
tuple val(prefix), path("*.fasta")
publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
task.ext.when == null || task.ext.when
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script:
def jmemstring = task.memory.toMega() + 'M'
"""
cliquesnv \\
-Xmx${jmemstring} \\
-threads ${task.cpus} \\
-m '${method}' \\
-in "${bam}" \\
-outDir .
"""
}