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Wip clarification usage #358

Merged
merged 3 commits into from
Apr 12, 2024
Merged

Wip clarification usage #358

merged 3 commits into from
Apr 12, 2024

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VErconi
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@VErconi VErconi commented Mar 20, 2024

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/atacseq 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).

@VErconi VErconi added enhancement New feature or request documentation labels Mar 20, 2024
@VErconi VErconi requested a review from bjlang March 20, 2024 14:55
bjlang
bjlang approved these changes Mar 20, 2024
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🚀

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github-actions bot commented Mar 20, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 357cf89

+| ✅ 170 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowAtacseq.groovy
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowAtacseq.groovy: Optionally add in-text citation tools to this list.
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 22]
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 35]

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-20 15:48:37

@VErconi
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VErconi commented Mar 20, 2024

This pull request contains an update of the usage.md file to address the following request of clarification #337

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bjlang commented Mar 20, 2024

@nf-core-bot fix linting

@VErconi VErconi closed this Mar 20, 2024
@VErconi VErconi reopened this Mar 20, 2024
JoseEspinosa
JoseEspinosa approved these changes Apr 12, 2024
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LGTM 🚀
Thanks a lot!

@JoseEspinosa
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Will merge with the lint error as the changes fixing it are already added in #360

@JoseEspinosa JoseEspinosa merged commit 9fbc9b0 into nf-core:dev Apr 12, 2024
13 of 22 checks passed
@bjlang bjlang mentioned this pull request Apr 12, 2024
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@bjlang bjlang bjlang approved these changes

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@VErconi @bjlang @JoseEspinosa @nf-core-bot