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mmassaviol
WAWmassaviol
Commits
c2680e81
Commit
c2680e81
authored
Oct 04, 2021
by
khalid
Browse files
debug htseq-count
parent
3bab8250
Changes
2
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tools/htseq_count/htseq_count.rule.snakefile
View file @
c2680e81
...
...
@@ -12,4 +12,4 @@ rule <step_name>__htseq_count:
htseq_orientation = config["<step_name>__htseq_orientation"],
output_dir = config["results_dir"]+'/'+config["<step_name>__htseq_count_output_dir"]
shell:
"{params.command} -f bam -a {params.htseq_count_minaqual} -s {params.htseq_stranded} -r {params.htseq_orientation} {input.bam} {input.gff_file} 2>
{log}
> {output.stats}"
"{params.command} -f bam -a {params.htseq_count_minaqual} -s {params.htseq_stranded} -r {params.htseq_orientation} {input.bam} {input.gff_file} 2>
>(tee -a {log} >&2)
> {output.stats}"
tools/htseq_count/htseq_count.yaml
View file @
c2680e81
...
...
@@ -7,7 +7,7 @@
description
:
"
A
tool
to
quantify
gene
expression
in
RNA-Seq
and
similar
experiments."
,
version
:
"
release_0.13.5"
,
documentation
:
"
https://htseq.readthedocs.io"
,
multiqc
:
"
htseq_count
"
,
multiqc
:
"
custom
"
,
commands
:
[
{
...
...
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