Mercurial > repos > eduardo > download_and_align
changeset 28:e0e38389a9cb draft default tip
Uploaded
author | eduardo |
---|---|
date | Tue, 04 Aug 2015 10:59:51 -0400 |
parents | 8f36fc727988 |
children | |
files | download_align.xml |
diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/download_align.xml Tue Aug 04 09:46:15 2015 -0400 +++ b/download_align.xml Tue Aug 04 10:59:51 2015 -0400 @@ -14,10 +14,10 @@ #else: #set index_path = $reference_genome.index.fields.path #end if - wget -O - $file | gunzip -c | cutadapt -q 20 - | bowtie2 -q + wget -O - $file | gunzip -c | cutadapt -q 20 -m 20 - | bowtie2 -q ## index file path -x $index_path - -U - | samtools view -b - > $output + -U - | samtools view -bS - > $output </command> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" />