Skip to content
Snippets Groups Projects
Verified Commit 18e214ae authored by Laurent Modolo's avatar Laurent Modolo
Browse files

cutadapt: fix bug :28

parent cfd74897
No related branches found
No related tags found
No related merge requests found
...@@ -19,13 +19,13 @@ process adaptor_removal { ...@@ -19,13 +19,13 @@ process adaptor_removal {
path "*_report.txt", emit: report path "*_report.txt", emit: report
script: script:
if (reads instanceof List) if (reads instanceof List) {
""" """
cutadapt ${params.adaptor_removal} \ cutadapt ${params.adaptor_removal} \
-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \ -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
""" """
else: } else {
""" """
cutadapt ${params.adaptor_removal} \ cutadapt ${params.adaptor_removal} \
-o ${file_id}_cut.fastq.gz \ -o ${file_id}_cut.fastq.gz \
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment