Sync some nf-core template files

.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
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/pixelator/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/pixelator/tree/main/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/pixelator/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/pixelator/tree/main/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/pixelator _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).

assets/sendmail_template.txt

@@ -26,6 +26,28 @@ Content-Disposition: inline; filename="nf-core-pixelator_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--