Commit 761fc5a5 authored by khalid's avatar khalid
Browse files

add a MBB logo to generated reports

parent c8ce2421
......@@ -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()
......
......@@ -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

18.8 KB

......@@ -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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