diff --git a/modules/04_vafator.nf b/modules/04_vafator.nf index 4a0f253..a0b4c78 100644 --- a/modules/04_vafator.nf +++ b/modules/04_vafator.nf @@ -23,12 +23,13 @@ process VAFATOR { script: bams_param = bams.collect { b -> "--bam " + b.split(":").join(" ") }.join(" ") - mq_param = "--mapping-quality " + params.mapping_quality - bq_param = "--base-call-quality " + params.base_call_quality """ vafator \ --input-vcf ${vcf} \ - --output-vcf ${vcf.baseName}.vaf.vcf ${bams_param} ${mq_param} ${bq_param} + --output-vcf ${vcf.baseName}.vaf.vcf \ + ${bams_param} \ + --mapping-quality ${params.mapping_quality} \ + --base-call-quality ${params.base_call_quality} """ }