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GTDB R07-RS207 #478

Merged
merged 6 commits into from Sep 6, 2022
Merged

GTDB R07-RS207 #478

merged 6 commits into from Sep 6, 2022

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erikrikarddaniel
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@erikrikarddaniel erikrikarddaniel commented Sep 5, 2022 •
edited

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
    • If necessary, also make a PR on the nf-core/ampliseq 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 --outdir <OUTDIR>).
  • 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).

I added both an entry for the official GTDB files, as well as our new SBDI-GTDB files.

There are a lot of linting warnings about when: condition has been removed.

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github-actions bot commented Sep 5, 2022 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7271f24

+| ✅ 151 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.5.1
  • Run at 2022-09-05 18:16:09

@d4straub
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d4straub commented Sep 6, 2022 •
edited

There are a lot of linting warnings about when: condition has been removed.

this means we lack a when statement in our modules. We do not use that whatsoever, but can be fixed before next release. Meaning: not important right now.

d4straub
d4straub approved these changes Sep 6, 2022
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LGTM!

@erikrikarddaniel erikrikarddaniel merged commit 73be82a into nf-core:dev Sep 6, 2022
@erikrikarddaniel erikrikarddaniel deleted the sbdi-gtdb-r207 branch September 6, 2022 08:14
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