Skip to content
Snippets Groups Projects
Verified Commit 6f027a2e authored by Laurent Modolo's avatar Laurent Modolo
Browse files

kallisto: fix warning in mapping_fastq about single-end parameters

parent 87dbf344
No related branches found
No related tags found
No related merge requests found
......@@ -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"
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment