diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf index d25f085a83668cdf4efa3e6eefceb349effca389..9c85118a3759eefd8eb680e886b70df909f47e29 100644 --- a/src/nf_modules/kallisto/main.nf +++ b/src/nf_modules/kallisto/main.nf @@ -50,22 +50,20 @@ process mapping_fastq { pair_id = file_id } - if (reads instanceof List) { + if (reads instanceof List) """ mkdir ${pair_id} kallisto quant -i ${index} -t ${task.cpus} \ ${params.mapping_fastq} -o ${pair_id} \ ${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_mapping_report.txt """ - } else { + else """ mkdir ${pair_id} kallisto quant -i ${index} -t ${task.cpus} --single \ ${params.mapping_fastq} -o ${pair_id} \ - -l ${params.mean} -s ${params.sd} \ ${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt """ - } } params.mapping_fastq_pairedend = "--bias --bootstrap-samples 100"