28 lines
576 B
Text
28 lines
576 B
Text
|
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"
|
||
|
|
"""
|
||
|
|
}
|