add soft version and summary in multiqc

assets/multiqc_config.yaml

@@ -3,7 +3,9 @@ report_comment: >
     analysis pipeline. For information about how to interpret these results, please see the
     <a href="https://forgemia.inra.fr/get-nextflow-ngl-bi/template-nf" target="_blank">documentation</a>.
 report_section_order:
-    nf-core/template-software-versions:
+    software_versions:
         order: -1000
+    summary:
+        order: -1001
 
 export_plots: true

bin/scrape_software_versions.py

@@ -5,13 +5,13 @@ import re
 
 # TODO nf-core: Add additional regexes for new tools in process get_software_versions
 regexes = {
-    'nf-core/template': ['v_pipeline.txt', r"(\S+)"],
+    'Pipeline': ['v_pipeline.txt', r"(\S+)"],
     'Nextflow': ['v_nextflow.txt', r"(\S+)"],
     'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"],
     'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"],
 }
 results = OrderedDict()
-results['nf-core/template'] = '<span style="color:#999999;\">N/A</span>'
+results['Pipeline'] = '<span style="color:#999999;\">N/A</span>'
 results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
 results['FastQC'] = '<span style="color:#999999;\">N/A</span>'
 results['MultiQC'] = '<span style="color:#999999;\">N/A</span>'
@@ -35,8 +35,7 @@ for k in results:
 # Dump to YAML
 print ('''
 id: 'software_versions'
-section_name: 'nf-core/template Software Versions'
-section_href: 'https://github.com/nf-core/template'
+section_name: 'Software Versions'
 plot_type: 'html'
 description: 'are collected at run time from the software output.'
 data: |

main.nf

@@ -228,6 +228,25 @@ process assembly {
     """
 }
 
+process workflow_summary {
+  
+  output:
+  file 'workflow_summary_mqc.yaml' into ch_workflow_summary_yaml
+
+  exec:
+  def yaml_file = task.workDir.resolve('workflow_summary_mqc.yaml')
+  yaml_file.text  = """
+  id: 'summary'
+  description: " - this information is collected when the pipeline is started."
+  section_name: 'Workflow Summary'
+  section_href: "${workflow.manifest.homePage}"
+  plot_type: 'html'
+  data: |
+        <dl class=\"dl-horizontal\">
+  ${summary.collect { k,v -> "            <dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }.join("\n")}
+        </dl>
+  """.stripIndent()
+}
 
 /*
  * STEP - MultiQC
@@ -243,8 +262,8 @@ process multiqc {
   file (multiqc_config) from ch_multiqc_config
   file ('fastqc/*') from ch_fastqc_results_for_multiqc.collect().ifEmpty([])
   // TODO get-nf: Add in log files from your new processes for MultiQC to find!
-  //file ('softwareVersions/*') from softwareVersionsYamlCh.collect().ifEmpty([])
-  //file ('workflowSummary/*') from workflowSummaryYamlCh.collect()
+  file ('software_versions/*') from software_versions_yaml.collect()
+  file ('workflowSummary/*') from ch_workflow_summary_yaml.collect()
 
   output: 
   file "*report.html" into ch_multiqc_report

nextflow.config

@@ -73,7 +73,7 @@ timeline {
 trace {
   enabled = true
   file = "${params.tracedir}/execution_trace.txt"
-  fields = 'task_id,name,status,exit,realtime,%cpu,rss,script'
+  fields = 'task_id,name,status,exit,realtime,%cpu,rss'
 }
 
 report {