Skip to content
Snippets Groups Projects
Verified Commit 170a745c authored by Laurent Modolo's avatar Laurent Modolo
Browse files

hisat2: change report file name

parent 600ee64e
No related branches found
No related tags found
No related merge requests found
......@@ -78,9 +78,9 @@ process mapping_fastq {
-2 ${reads[1]} 2> \
${file_prefix}_ht2_mapping_report.txt \
| samtools view -@ ${task.cpus} -bS - 2>> \
${file_prefix}_ht2_mapping_report.txt \
${file_prefix}_ht2_samtools_view_report.txt \
| samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
${file_prefix}_ht2_mapping_report.txt
${file_prefix}_ht2_samtools_sort_report.txt
if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
exit 1
......@@ -94,9 +94,9 @@ process mapping_fastq {
-U ${reads} 2> \
${file_prefix}_ht2_mapping_report.txt \
| samtools view -@ ${task.cpus} -bS - 2>> \
${file_prefix}_ht2_mapping_report.txt \
${file_prefix}_ht2_samtools_view_report.txt \
| samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
${file_prefix}_ht2_mapping_report.txt
${file_prefix}_ht2_samtools_sort_report.txt
if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
exit 1
......
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