add a MBB logo to generated reports

generate_multiqc_config.py

@@ -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

@@ -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"]:

tools/radsex_processTagged/radsex_processTagged.rule.snakefile

@@ -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