Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
mmassaviol
WAWmassaviol
Commits
e7dd4dff
Commit
e7dd4dff
authored
Oct 04, 2021
by
khalid
Browse files
debug raw_gff3
parent
a18cc47b
Changes
5
Hide whitespace changes
Inline
Side-by-side
generate_workflow_snakefile.py
View file @
e7dd4dff
...
...
@@ -79,7 +79,7 @@ def generate(name, path_yaml = "", path_input = DEFAULT_PATH_INPUT, path_output
result
+=
"config.update("
+
raw_input
+
")
\n
"
# !!! possibilité de définir samples plusieurs fois si il y a raw_reads et raw_vcf ... !!!
# il faut vérifier que les samples sont les mêmes ?
if
not
raw_input
.
endswith
(
"_index"
)
and
not
raw_input
.
endswith
(
"_popmap"
)
and
not
raw_input
.
endswith
(
"_vcfFile"
):
if
not
raw_input
.
endswith
(
"_index"
)
and
not
raw_input
.
endswith
(
"_popmap"
)
and
not
raw_input
.
endswith
(
"_vcfFile"
)
and
not
raw_input
.
endswith
(
"_gff3"
)
:
result
+=
"SAMPLES = "
+
raw_input
+
"['samples']
\n
"
result
+=
"
\n
"
...
...
raw_inputs/raw_gds.yaml
View file @
e7dd4dff
{
name
:
raw_gds
,
function_call
:
"
raw_gds(config['results_dir'],
config['
gds_file
'])"
,
function_call
:
"
raw_gds(config['results_dir'],
config['
sample_dir
'])"
,
options
:
[
{
name
:
"
gds_file"
,
...
...
raw_inputs/raw_gff3.py
View file @
e7dd4dff
...
...
@@ -2,10 +2,10 @@ import os
import
re
import
sys
def
raw_
vcf
(
results_dir
,
sample
_dir
):
def
raw_
gff3
(
results_dir
,
input
_dir
):
samples
=
list
()
out
=
dict
()
out
[
"g
ds
"
]
=
input_dir
out
[
"g
ff3
"
]
=
input_dir
return
out
...
...
raw_inputs/raw_gff3.yaml
View file @
e7dd4dff
...
...
@@ -3,8 +3,8 @@
function_call
:
"
raw_gff3(config['results_dir'],
config['sample_dir'])"
,
options
:
[
{
name
:
"
sample_dir
"
,
type
:
"
input_
dir
"
,
name
:
"
gff_file
"
,
type
:
"
input_
file
"
,
value
:
"
/Data"
,
label
:
"
gff3
file:
"
,
volumes
:
[
Data
:
"
/Data"
,
Results
:
"
/Results"
]
...
...
tools/htseq_count/htseq_count.rule.snakefile
View file @
e7dd4dff
...
...
@@ -7,8 +7,8 @@ rule <step_name>__htseq_count:
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"],
htseq_count_minaqual = config["
<step_name>__
htseq_count_minaqual"],
htseq_stranded = config["
<step_name>__
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}"
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment