diff --git a/modules/quasirecomb/main.nf b/modules/quasirecomb/main.nf new file mode 100644 index 0000000..e2896c0 --- /dev/null +++ b/modules/quasirecomb/main.nf @@ -0,0 +1,27 @@ +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" + """ +}