Skip to content
Snippets Groups Projects
Commit 71c8b121 authored by Xavier Grand's avatar Xavier Grand
Browse files

Modify samtools/main.nf AS filter from 500 to 100.

parent 372438ee
No related branches found
No related tags found
No related merge requests found
......@@ -102,12 +102,12 @@ process filter_as {
tuple val(barcode), path(bam)
output:
tuple val(barcode), path("${barcode}/*_AS500.bam"), emit: filtered_bam
tuple val(barcode), path("${barcode}/*_AS100.bam"), emit: filtered_bam
script:
"""
mkdir ${barcode}
cd ${barcode}/
samtools view -Shb -e '[AS]>=500' -@ ${task.cpus} ../${bam} -o ${barcode}_AS500.bam
samtools view -Shb -e '[AS]>=100' -@ ${task.cpus} ../${bam} -o ${barcode}_AS100.bam
"""
}
\ No newline at end of file
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