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Fix prefix for eukulele columns in summary #180

Merged
merged 2 commits into from
Sep 13, 2023
Merged

Fix prefix for eukulele columns in summary #180

merged 2 commits into from
Sep 13, 2023

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erikrikarddaniel
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PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

This fixes issue #179 . I also did a bit of cleaning up of the R code.

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github-actions bot commented Sep 13, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 44ae6ef

+| ✅ 154 tests passed       |+
!| ❗   7 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 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 output.md: Write this documentation describing your workflow's output
  • 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 2.9
  • Run at 2023-09-13 13:27:35

emnilsson
emnilsson approved these changes Sep 13, 2023
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LGTM, haven't tested it though, and one tiny question.

subworkflows/local/eukulele.nf Outdated
Comment on lines 37 to 38
ch_sum_taxonomy.view()
feature_counts.view()
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Should these really be in here? I don't see any issue with .view, it's just that I've mostly used it to verify code.

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Thanks, should not be there of course!

@erikrikarddaniel erikrikarddaniel merged commit ca5de38 into nf-core:dev Sep 13, 2023
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@erikrikarddaniel erikrikarddaniel deleted the fix-eukulele-field-name branch September 13, 2023 13:26
@erikrikarddaniel erikrikarddaniel mentioned this pull request Sep 13, 2023
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@emnilsson emnilsson emnilsson approved these changes

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@erikrikarddaniel @emnilsson