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Merging template updates 2.0.1#218

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skrakau merged 14 commits intonf-core:devfrom
skrakau:merging-template-updates-2.0.1
Jul 26, 2021
Merged

Merging template updates 2.0.1#218
skrakau merged 14 commits intonf-core:devfrom
skrakau:merging-template-updates-2.0.1

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@skrakau skrakau commented Jul 24, 2021 •
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Merge template updates 2.0.1:

  • changed a few output paths due to publish_by_id -> publish_by_meta and adjusted this accordingly in the output.md (the generation of custom paths specified before withpublish_id: 'bla_${meta.id}' did not work anymore like this)
  • adjusted .editorconfig as in template dev branch to avoid lint test to fail (nf-core/tools@d7ebfa1)
  • and changed path to testdata to https://raw.githubusercontent.com/nf-core/test-datasets instead of using https://github.com/nf-core/test-datasets/raw

(Note, I accidentally started the template updates on the wrong branch containing commits regarding Prodigal which are now already merged into dev #217. However, GitHub doesn't detect those changes in dev, but it should be fine when merging. So the commits Publish genes predicted with Prodigal in BUSCO process, Mention prodigal output in docs, Update CHANGELOG can be ignored.)

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions Bot commented Jul 24, 2021 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 3c4148c

+| ✅ 137 tests passed       |+
#| ❔   1 tests were ignored |#
Details

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.0.1
  • Run at 2021-07-26 07:16:17

@skrakau skrakau requested a review from ggabernet July 24, 2021 17:07
ggabernet
ggabernet approved these changes Jul 25, 2021
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Hi @skrakau, it is looking good to me, I just had a couple of comments :)

Comment thread conf/docker.config Outdated
Comment thread nextflow.config Outdated
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skrakau commented Jul 26, 2021

Thanks a lot @ggabernet !

@skrakau skrakau merged commit 45286d9 into nf-core:dev Jul 26, 2021
@skrakau skrakau deleted the merging-template-updates-2.0.1 branch July 22, 2022 09:21
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@ggabernet ggabernet ggabernet approved these changes

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@skrakau @ggabernet @KevinMenden @nf-core-bot