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mmassaviol
WAWmassaviol
Commits
56971a55
Commit
56971a55
authored
Oct 04, 2021
by
khalid
Browse files
Add a group_file inpput to edger and deseq2
parent
1457d60f
Changes
4
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Inline
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tools/deseq2/deseq2.yaml
View file @
56971a55
...
...
@@ -16,7 +16,8 @@
command
:
~
,
category
:
"
differential_expression"
,
output_dir
:
deseq2
,
inputs
:
[{
name
:
counts
,
type
:
"
tsv"
}],
inputs
:
[{
name
:
counts
,
type
:
"
tsv"
}
{
name
:
group_file
,
type
:
"
popmap"
,
file
:
"
"
,
description
:
"
Path
to
tsv
file
with
samples
conditions"
}],
outputs
:
[
{
name
:
de_table
,
type
:
"
tsv"
,
file
:
de_table.csv
,
description
:
"
Tableau
d'expression
différentielle"
},
...
...
tools/edger/edger.yaml
View file @
56971a55
...
...
@@ -15,7 +15,9 @@
command
:
~
,
category
:
"
differential_expression"
,
output_dir
:
edger
,
inputs
:
[{
name
:
counts
,
type
:
"
tsv"
}],
inputs
:
[{
name
:
counts
,
type
:
"
tsv"
},
{
name
:
group_file
,
type
:
"
popmap"
,
file
:
"
"
,
description
:
"
Path
to
tsv
file
with
samples
conditions"
},
]
outputs
:
[
{
name
:
de_table
,
type
:
"
csv"
,
file
:
de_table.csv
,
description
:
"
Tableau
d'expression
différentielle"
},
...
...
tools/hisat2/hisat2.rule.snakefile
View file @
56971a55
...
...
@@ -18,7 +18,7 @@ if config["SeOrPe"] == "PE":
maxins = config["<step_name>__hisat2_maxins_PE"],
orientation = config["<step_name>__hisat2_orientation_PE"],
shell:
"{params.command} "
"{params.command}
--new-summary
"
"--threads {threads} "
"-x {params.indexPrefix} "
"-I {params.minins} "
...
...
tools/htseq_count/htseq_count.yaml
View file @
56971a55
...
...
@@ -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
:
"
htseq"
,
commands
:
[
{
...
...
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