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mmassaviol
WAWmassaviol
Commits
506f0f69
Commit
506f0f69
authored
Oct 04, 2021
by
khalid
Browse files
Add htseq-count
parent
761fc5a5
Changes
2
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tools/htseq-count/htseq-count.rule.snakefile
0 → 100644
View file @
506f0f69
rule <step_name>__htseq-count:
input:
**<step_name>__htseq-count_inputs()
output:
stats = config["results_dir"]+'/' + config["<step_name>__htseq-count_output_dir"] + '/{sample}.txt',
log:
config["results_dir"]+'/logs/' + config["<step_name>__htseq-count_output_dir"] + '/{sample}_htseq-count_log.txt'
params:
command = config["<step_name>__htseq-count_command"],
htseq-count_minaqual = config["htseq-count_minaqual"],
htseq_stranded = config["htseq_stranded"],
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}"
tools/htseq-count/htseq-count.yaml
0 → 100644
View file @
506f0f69
{
id
:
htseq-count
,
name
:
Htseq-count
,
article
:
doi
:
10.1093/bioinformatics/btu638
,
website
:
"
https://htseq.readthedocs.io"
,
git
:
"
https://github.com/htseq/htseq"
,
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"
,
commands
:
[
{
name
:
htseq-count
,
command
:
htseq-count
,
category
:
"
quantification"
,
output_dir
:
htseq-count
,
inputs
:
[
{
name
:
bam
,
type
:
"
bams"
},
{
name
:
gff_file
,
type
:
"
gff3"
}
],
outputs
:
[
{
name
:
stats
,
type
:
"
txt"
,
file
:
"
{sample}_htseq-count.txt"
,
description
:
"
a
table
with
counts
for
each
feature"
}
],
options
:
[
{
name
:
htseq-count_minaqual
,
prefix
:
-a
,
type
:
numeric
,
value
:
10
,
min
:
1
,
max
:
80
,
step
:
1
,
label
:
"
skip
all
reads
with
alignment
quality
lower
than
the
given
minimum
value"
,
},
{
name
:
htseq_stranded
,
type
:
radio
,
choices
:
[
Not stranded
:
"
no"
,
Stranded
:
"
yes"
,
Reverse Stranded
:
"
reverse"
,
],
value
:
"
no"
,
label
:
"
whether
the
data
is
from
a
strand-specific
assay."
,
},
{
name
:
htseq_orientation
,
type
:
radio
,
choices
:
[
Position
:
"
position"
,
Name
:
"
name"
],
value
:
"
position"
,
label
:
"
the
way
that
alignment
have
been
sorted
(either
by
read
name
or
by
alignment
position)."
,
},
],
},
],
install
:
{
htseq
:
[
"
pip3
install
"
HTSeq==0.13.5"
]
},
citations
:
{
htseq
:
[
"
Simon
Anders,
Paul
Theodor
Pyl,
Wolfgang
Huber.
HTSeq
-
A
Python
framework
to
work
with
high-throughput
sequencing
data
Bioinformatics
(2014)."
]
}
}
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