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Reorder & rename prokka cols, save output to better named file #213

Merged
merged 3 commits into from
Nov 28, 2023
Merged

Reorder & rename prokka cols, save output to better named file #213

merged 3 commits into from
Nov 28, 2023

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erikrikarddaniel
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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/metatdenovo 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).

Make sure columns are lowcase and come in alphabetical order (from col 9) to increase chances that different tables from a complex project can be read in the same read_tsv call. Rename the output to be more descriptive.

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github-actions bot commented Nov 27, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2f5726e

+| ✅ 156 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.5.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-27 20:56:07

danilodileo
danilodileo approved these changes Nov 28, 2023
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LGTM

@danilodileo danilodileo merged commit 601a673 into nf-core:dev Nov 28, 2023
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@danilodileo danilodileo danilodileo approved these changes

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@erikrikarddaniel @danilodileo