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Sync some nf-core template files
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fbdtemme committed Dec 13, 2024
1 parent dd40572 commit e15a0d1
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2 changes: 2 additions & 0 deletions .github/CONTRIBUTING.md
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Expand Up @@ -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

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4 changes: 2 additions & 2 deletions .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -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>`).
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22 changes: 22 additions & 0 deletions assets/sendmail_template.txt
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Expand Up @@ -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--

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