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More cohesion between subworkflows #583

Merged
merged 2 commits into from
Jun 9, 2022
Merged

More cohesion between subworkflows #583

merged 2 commits into from
Jun 9, 2022

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maxulysse
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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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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).

@maxulysse maxulysse changed the title code polish More cohesion between subworkflows Jun 9, 2022
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github-actions bot commented Jun 9, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5fa3eea

+| ✅ 144 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 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
  • schema_description - No description provided in schema for parameter: umi_read_structure
  • schema_description - No description provided in schema for parameter: group_by_umi_strategy

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-09 11:36:08

WackerO
WackerO approved these changes Jun 9, 2022
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That went quick!

@FriederikeHanssen
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i think it just glitched earlier. Merge?

@maxulysse maxulysse merged commit ba1b991 into nf-core:dev Jun 9, 2022
@maxulysse maxulysse deleted the dev_polish branch June 9, 2022 12:39
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@WackerO WackerO WackerO approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen @WackerO