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Collect stats bug #189

Merged
merged 2 commits into from
Sep 29, 2023
Merged

Collect stats bug #189

merged 2 commits into from
Sep 29, 2023

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danilodileo
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@danilodileo danilodileo commented Sep 29, 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).

I made a small PR to fix a bug in collect stats. It was unable to provide output when ´--se_ends´was provided. I tested all combination with and without the parameter and now it works.

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github-actions bot commented Sep 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 43eaad2

+| ✅ 156 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-09-29 03:40:39

erikrikarddaniel
erikrikarddaniel approved these changes Sep 29, 2023
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👍

@danilodileo danilodileo merged commit ff3b473 into nf-core:dev Sep 29, 2023
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@danilodileo danilodileo deleted the collect_stats_bug branch September 29, 2023 05:25
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@danilodileo @erikrikarddaniel