Verified Commit 1c82c356 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

Kallisto.nf: fix paired name

parent a97e28f0
......@@ -54,12 +54,12 @@ Channel
.set { index_files }
process mapping_fastq {
tag "$pair_id"
tag "$reads"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
file reads from fastq_files
file index from index_files.toList()
output:
......@@ -67,9 +67,9 @@ process mapping_fastq {
script:
"""
mkdir ${pair_id}
mkdir ${reads[0].baseName}
kallisto quant -i ${index} -t ${task.cpus} \
--bias --bootstrap-samples 100 -o ${pair_id} \
--bias --bootstrap-samples 100 -o ${reads[0].baseName} \
${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
"""
}
......
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