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Modules updates: Bakta, AMRFinderPlus, and MultiQC #308

Merged
merged 6 commits into from
Oct 5, 2023
Merged

Modules updates: Bakta, AMRFinderPlus, and MultiQC #308

merged 6 commits into from
Oct 5, 2023

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jasmezz
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@jasmezz jasmezz commented Aug 30, 2023

Updating these modules:

  • bakta/main and bakta/baktadbdownload
  • amrfinderplus/run and amrfinderplus/update
  • multiqc (and it's version number the dumpsoftwareversions module)

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/funcscan 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).

@jasmezz jasmezz requested a review from a team August 30, 2023 15:19
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github-actions bot commented Aug 30, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5e7cc6b

+| ✅ 159 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-02 12:16:26

jfy133
jfy133 reviewed Sep 28, 2023
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@jfy133 jfy133 self-requested a review October 4, 2023 10:13
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jfy133 commented Oct 4, 2023

Maybe we need to make a mirror of these stupid databases (e.g. on dropbox or something)

@jasmezz
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jasmezz commented Oct 5, 2023

Yeah just in this case, it is the "no space left on device" error, which a mirror wouldn't solve 🥲

@jasmezz jasmezz merged commit 522ca9d into dev Oct 5, 2023
15 of 20 checks passed
@jasmezz jasmezz deleted the modules_update branch October 5, 2023 08:14
@jasmezz jasmezz mentioned this pull request Nov 13, 2023
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@jfy133 jfy133 jfy133 approved these changes

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@jasmezz @jfy133