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

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process QUASIRECOMB {
tag "${prefix}"
label 'process_high'
container 'quay.io/biocontainers/quasirecomb:1.2--hdfd78af_1'
input:
tuple val(prefix), path(bam)
output:
tuple val(prefix), path("*.fasta")
publishDir "results/${task.process}", mode: 'copy'
script:
def jmemstring = task.memory.toMega() + 'M'
"""
quasirecomb \\
-XX:+UseParallelGC \\
-Xms2g \\
-Xmx${jmemstring} \\
-XX:+UseNUMA \\
-XX:NewRatio=9 \\
-i "${bam}"
mv quasispecies.fasta "${prefix}.fasta"
"""
}