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Modules update incl. fixing pigz in Pyrodigal #299

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merged 4 commits into from
Aug 2, 2023
Merged

Modules update incl. fixing pigz in Pyrodigal #299

merged 4 commits into from
Aug 2, 2023

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jasmezz
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@jasmezz jasmezz commented Jul 28, 2023 •
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Pull some updated modules.
Pyrodigal: Fix pigz symlink issue, closes #291
GECCO: Due to renamed column in output file, comBGC had to be adjusted.

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 July 28, 2023 09:09
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github-actions bot commented Jul 28, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 36fc195

+| ✅ 157 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 2.9
  • Run at 2023-08-02 13:27:00

@jasmezz jasmezz changed the title Modules update Modules update incl. fix of pigz in Pyrodigal Jul 28, 2023
@jasmezz jasmezz changed the title Modules update incl. fix of pigz in Pyrodigal Modules update incl. fixing pigz in Pyrodigal Jul 28, 2023
jfy133
jfy133 reviewed Jul 28, 2023
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CHANGELOG.md Outdated

### `Dependencies`

| Tool | Previous version | New version |
| ----- | ---------------- | ----------- |
| GECCO | 0.9.2 | 0.9.8 |
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Where are the version updates for the other tools? Have you validated the working correctly?

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Added comBGC. 👍 The other modules (fastqc, gunzip, pyrodigal, untar) are just changes in the nf-core module, not actually version updates. And yes, all modules work correctly.

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jasmezz commented Aug 2, 2023

DeepARG workflow fails because deepARG download server is down again 😐

@jasmezz jasmezz requested a review from jfy133 August 2, 2023 12:01
jfy133
jfy133 approved these changes Aug 2, 2023
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@jasmezz @jfy133
Update CHANGELOG.md
36fc195 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@jasmezz jasmezz merged commit fadc05c into dev Aug 2, 2023
16 of 24 checks passed
@jasmezz jasmezz deleted the modules-update branch August 2, 2023 14:39
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@jasmezz @jfy133