diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf index 531db710..1f940d67 100644 --- a/software/ivar/variants/main.nf +++ b/software/ivar/variants/main.nf @@ -29,10 +29,10 @@ process IVAR_VARIANTS { path "*.version.txt" , emit: version script: - def software = getSoftwareName(task.process) - def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" - def save_mpileup = params.containsKey('save_mpileup') ? "tee ${prefix}.mpileup |" : "" - def gff = params.containsKey('gff') ? "-g ${params.get('gff')}" : "" + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : "" + def features = params.gff ? "-g $gff" : "" """ samtools mpileup \\ $options.args2 \\