Commit 9ad0c962 authored by Amine  GHOZLANE's avatar Amine GHOZLANE

Debug missing information

parent f6ed03f2
......@@ -106,19 +106,9 @@ process fastqfiltering {
--un !{sample_id}_notmapped_mouse.fastq > !{sample_id}_mapping_mouse.txt 2>&1
bowtie2 -p !{params.cpus} --sensitive-local -x !{params.phi}\
-U !{sample_id}_notmapped_mouse.fastq -S /dev/null \
--un !{sample_id}_notmapped.fastq > !{sample_id}_mapping_phi.txt 2>&1
case "!{reads}" in
*.gz )
nb_raw=\$(echo \$((\$(gunzip -c !{reads} | wc -l) / 4)))
echo -e "Number of raw reads\t\$nb_raw" > !{sample_id}_resume_nb_reads.txt
;;
*.fastq)
nb_raw=\$(echo \$((`wc -l < !{reads}` / 4)))
echo -e "Number of raw reads\t\$nb_raw" > !{sample_id}_resume_nb_reads.txt
;;
esac
--un !{sample_id}_notmapped.fastq > !{sample_id}_mapping_phi.txt 2>&1
nb_raw=\$(echo \$((`wc -l < !{reads}` / 4)))
echo -e "Number of raw reads\t\$nb_raw" > !{sample_id}_resume_nb_reads.txt
nb_filt=\$(echo \$((`wc -l < !{sample_id}_notmapped.fastq` / 4)))
echo -e "Number of reads after filtering\t\$nb_filt" >> !{sample_id}_resume_nb_reads.txt
"""
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment