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mmassaviol
WAWmassaviol
Commits
761fc5a5
Commit
761fc5a5
authored
Oct 01, 2021
by
khalid
Browse files
add a MBB logo to generated reports
parent
c8ce2421
Changes
4
Hide whitespace changes
Inline
Side-by-side
generate_multiqc_config.py
View file @
761fc5a5
...
...
@@ -83,6 +83,11 @@ def report_section_order():
def
main
():
res
=
"skip_generalstats: true
\n\n
"
res
+=
"report_comment: '"
+
config
[
"params"
][
"memo"
]
+
"'
\n\n
"
res
+=
"custom_logo: /workflow/mbb.png
\n\n
"
res
+=
"custom_logo_url: https://mbb.univ-montp2.fr
\n\n
"
res
+=
"custom_logo_title: MBB platform
\n\n
"
res
+=
module_order
()
+
"
\n\n
"
res
+=
report_section_order
()
+
"
\n\n
"
res
+=
files_or_dirs_to_ignore
()
...
...
generate_workflow.py
View file @
761fc5a5
...
...
@@ -428,6 +428,7 @@ def generate_pipeline_files(workflow_yaml, output_dir, waw_dir, local_config="de
shutil
.
copy
(
os
.
path
.
join
(
waw_dir
+
"/generate_multiqc_config.py"
),
output_dir
+
"/files"
)
shutil
.
copy
(
os
.
path
.
join
(
waw_dir
+
"/tools.py"
),
output_dir
+
"/files"
)
shutil
.
copy
(
os
.
path
.
join
(
waw_dir
+
"/mbb.png"
),
output_dir
+
"/files"
)
if
"input"
in
WORKFLOW_YAML
:
for
raw_input
in
WORKFLOW_YAML
[
"input"
]:
...
...
mbb.png
0 → 100644
View file @
761fc5a5
18.8 KB
tools/radsex_processTagged/radsex_processTagged.rule.snakefile
View file @
761fc5a5
...
...
@@ -16,28 +16,4 @@ rule <step_name>__radsex_processTagged:
"--popmap {input.popmap_file} "+
"-T {threads} "+
"-o {output} "+
"-d {params.min_depth}; "
# + """awk "
# {{
# # if(NR==FNR ){{
# if (NR ==2 ) {{nbFields = NF}}
# if (NR > 2) for (i = 3; i <= NF; i++) a[i]+=\$i;
# }}
# else {{ # reading second file
# if (FNR == 1)
# {{
# print \$0
# for (i = 3; i <= nbFields; i++) a[i] = a[i] / 1000000; #per million
# }}
# if (FNR == 2) for (i = 1; i <= nbFields; i++) printf \\"%s\\t\\",\$i;
# print \\"\\"
# if (FNR > 2)
# {{
# printf \\"%s\\t%s\\t\\",\$1,\$2
# for (i = 3; i <= nbFields; i++) printf \\"%s\\t\\",int(\$i/a[i]);
# print \\"\\"
# }}
# }}
# }}" {output} {output} > tmp.cpm ; """ +
# "mv tmp.cpm {output}"
"-d {params.min_depth}; "
\ No newline at end of file
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