Fix MultiQC inclusion

.github/CONTRIBUTING.md

@@ -79,6 +79,8 @@ If you wish to contribute a new step, please use the following coding standards:
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
 

assets/sendmail_template.txt

@@ -26,6 +26,28 @@ Content-Disposition: inline; filename="nf-core-bamtofastq_logo_light.png"
     join( '\n' ) %>
 
 <%
+if (mqcFile){
+def mqcFileObj = new File("$mqcFile")
+if (mqcFileObj.length() < mqcMaxSize){
+out << """
+--nfcoremimeboundary
+Content-Type: text/html; name=\"multiqc_report\"
+Content-Transfer-Encoding: base64
+Content-ID: <mqcreport>
+Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
+
+${mqcFileObj.
+    bytes.
+    encodeBase64().
+    toString().
+    tokenize( '\n' )*.
+    toList()*.
+    collate( 76 )*.
+    collect { it.join() }.
+    flatten().
+    join( '\n' )}
+"""
+}}
 %>
 
 --nfcoremimeboundary--

nextflow.config

@@ -24,6 +24,13 @@ params {
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
 
+    // MultiQC options
+    multiqc_config              = null
+    multiqc_title               = null
+    multiqc_logo                = null
+    max_multiqc_email_size      = '25.MB'
+    multiqc_methods_description = null
+
     // Boilerplate options
     outdir                       = null
     publish_dir_mode             = 'copy'

nextflow_schema.json

@@ -205,6 +205,14 @@
                     "fa_icon": "fas fa-remove-format",
                     "hidden": true
                 },
+                "max_multiqc_email_size": {
+                    "type": "string",
+                    "description": "File size limit when attaching MultiQC reports to summary emails.",
+                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
+                    "default": "25.MB",
+                    "fa_icon": "fas fa-file-upload",
+                    "hidden": true
+                },
                 "monochrome_logs": {
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",