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

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2023-09-23 21:40:04 +00:00
process CLIQUESNV {
tag "${prefix}"
label 'process_high'
container 'quay.io/biocontainers/cliquesnv:2.0.3--hdfd78af_0'
input:
tuple val(prefix), path(bam)
val(method)
output:
tuple val(prefix), path("*.json")
tuple val(prefix), path("*.fasta")
publishDir "results/${task.process}", mode: 'copy'
script:
def jmemstring = task.memory.toMega() + 'M'
"""
cliquesnv \\
-Xmx${jmemstring} \\
-threads ${task.cpus} \\
-m '${method}' \\
-in "${bam}" \\
-outDir .
"""
}