diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf index 43425ca5..de9e8b3d 100644 --- a/software/bowtie/align/main.nf +++ b/software/bowtie/align/main.nf @@ -27,12 +27,11 @@ process BOWTIE_ALIGN { tuple val(meta), path('*.out'), emit: log path '*.version.txt' , emit: version tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq - path 'test.txt', emit: test script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" - def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : '' + def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : '' def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}" """ INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'` @@ -47,7 +46,6 @@ process BOWTIE_ALIGN { 2> ${prefix}.out \\ | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam - - touch test.txt if [ -f ${prefix}.unmapped.fastq ]; then gzip ${prefix}.unmapped.fastq fi