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Output concatenated ffn files from Prokka #186

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merged 2 commits into from
Sep 26, 2023
Merged

Output concatenated ffn files from Prokka #186

merged 2 commits into from
Sep 26, 2023

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erikrikarddaniel
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@erikrikarddaniel erikrikarddaniel commented Sep 26, 2023 •
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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).

We didn't output the ffn file (features in nucleotide fasta format) from Prokka, but only the fna (contigs). (The latter is actually not necessary as it's identical to the output from the assembly program, but I kept it.)

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github-actions bot commented Sep 26, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit be351ba

+| ✅ 150 tests passed       |+
!| ❗   7 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • files_unchanged - CODE_OF_CONDUCT.md does not match the template
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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 2023-09-26 12:04:09

emnilsson
emnilsson approved these changes Sep 26, 2023
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LGTM, but - what's the point of keeping the fna if it's identical to the one from assembly? If we have that one published from the assembly? I'd vote for removing one of them, rather than taking up space for the same thing.

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I agree @emnilsson , so I've removed it.

Linting is failing because of the template update. I'm overriding this here.

@erikrikarddaniel erikrikarddaniel merged commit 36157f5 into nf-core:dev Sep 26, 2023
6 of 7 checks passed
@erikrikarddaniel erikrikarddaniel deleted the cat-prokka-ffn branch September 26, 2023 12:47
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@erikrikarddaniel @emnilsson