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Remote test warning from nf-core lint #894

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merged 5 commits into from
Dec 12, 2022
Merged

Remote test warning from nf-core lint #894

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33f2652
add description to --cnvkit_reference
maxulysse Dec 12, 2022
59842ca
update CHANGELOG
maxulysse Dec 12, 2022
6a3b374
Remove methods description TODO prompt
maxulysse Dec 12, 2022
ab2749b
update CHANGELOG
maxulysse Dec 12, 2022
4ac0b43
json internal structure was rebuilt by nf-core tools
maxulysse Dec 12, 2022
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -24,6 +24,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#870](https://github.com/nf-core/sarek/pull/870) - Fix output for locally realigned reads from haplotypecaller
- [#874](https://github.com/nf-core/sarek/pull/874) - Remove `CITATION.cff`
- [#894](https://github.com/nf-core/sarek/pull/894) - Add description to --cnvkit_reference
- [#894](https://github.com/nf-core/sarek/pull/894) - Remove methods description TODO prompt

### Deprecated

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2 changes: 0 additions & 2 deletions assets/methods_description_template.yml
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Expand Up @@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
section_name: "nf-core/sarek Methods Description"
section_href: "https://github.com/nf-core/sarek"
plot_type: "html"
## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
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shouldn't we add some description on sarek here?

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I looked at the other pipelines, and nothing is there, the only difference I saw in some pipelines was the comments removed.
I'm not sure why it's in the TEMPLATE

## You inject any metadata in the Nextflow '${workflow}' object
data: |
<h4>Methods</h4>
<p>Data was processed using nf-core/sarek v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
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8 changes: 4 additions & 4 deletions modules.json
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Expand Up @@ -10,14 +10,14 @@
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": ["modules"]
},
"bcftools/mpileup": {
"bcftools/concat": {
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"branch": "master",
"git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": ["modules"]
},
"bcftools/concat": {
"bcftools/mpileup": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe",
"installed_by": ["modules"]
},
"bcftools/sort": {
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4 changes: 3 additions & 1 deletion nextflow_schema.json
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Expand Up @@ -347,7 +347,9 @@
"type": "string",
"default": null,
"fa_icon": "fas fa-file",
"help_text": "https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=reference.cnn#batch"
"help_text": "https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=reference.cnn#batch",
"description": "Copy-number reference for CNVkit",
"hidden": true
},
"pon": {
"type": "string",
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