Fix config for references.

workflow/conf/multiqc_config.yaml

+# Title to use for the report.
+title: BICF ChIP-seq Analysis Report
+
+report_comment: >
+    This report has been generated by the <a href="https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/" target="_blank">BICF/chipseq_analysis</a>
+    pipeline.
+
+report_section_order:
+    software_versions:
+        order: -1000
+
+report_section_order:
+    software_references:
+        order: -1000
+
+extra_fn_clean_exts:
+    - '_R1'
+    - '_R2'
+    - 'pbc.qc'
+
+fn_ignore_files:
+    - '*dedup.flagstat.qc'
+
+custom_data:
+    library_complexity:
+      file_format: 'tsv'
+      id: 'library_complexity'
+      contents: 'TotalReadPairs  DistinctReadPairs       OneReadPair     TwoReadPairs    NRF     PBC1    PBC2'
+      section_name: 'Library complexity'
+      plot_type: 'generalstats'
+
+sp:
+    phantompeakqualtools/out:
+        fn: '*cc.qc'
+    library_complexity:
+        fn: '*pbc.qc'

workflow/main.nf

@@ -505,8 +505,8 @@ process softwareReport {
 
   output:
 
-  file('*_mqc.yaml') into softwareVersions
-  file('*_mqc.txt') into softwareReferences
+  file('software_versions_mqc.yaml') into softwareVersions
+  file('software_references_mqc.yaml') into softwareReferences
 
   script:
   """

workflow/scripts/generate_references.py

@@ -44,20 +44,21 @@ def main():
     reference = args.reference
     output = args.output
 
-    out_filename = output + '_mqc.txt'
+    out_filename = output + '_mqc.yaml'
 
     # Header for HTML
     print('''
-        # id: 'References'
-        # section_name: 'References'
-        # description: 'This section describes references for the tools used.'
-        # plot_type: 'html'
+        id: 'Software References'
+        section_name: 'Software References'
+        description: 'This section describes references for the tools used.'
+        plot_type: 'html'
+        data: |
         '''
     , file = open(out_filename, "w")
     )
 
     # Turn Markdown into HTML
-    references_html = 'bash -c "pandoc {} >> {}"'
+    references_html = 'bash -c "pandoc -p {} | sed \'s/^/                /\' >> {}"'
     references_html = references_html.format(reference, out_filename)
     subprocess.check_call(shlex.split(references_html))