diff --git a/src/nf_modules/cutadapt/main.nf b/src/nf_modules/cutadapt/main.nf index a4d08fe873bec6478a3807196376836178ba4391..3307dd40ad35382fc25fc3d639052e3cfda1aacf 100644 --- a/src/nf_modules/cutadapt/main.nf +++ b/src/nf_modules/cutadapt/main.nf @@ -19,18 +19,19 @@ process adaptor_removal { path "*_report.txt", emit: report script: -if (reads instanceof List) { + if (reads instanceof List) { """ cutadapt ${params.adaptor_removal} \ -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \ ${reads[0]} ${reads[1]} > ${pair_id}_report.txt """ -} else { + } else { """ cutadapt ${params.adaptor_removal} \ -o ${file_id}_cut.fastq.gz \ ${reads} > ${file_id}_report.txt """ + } } params.adaptor_removal_pairedend = "-a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim}"