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Fix double slash in directory urls #355

Merged
merged 1 commit into from
Mar 20, 2024
Merged

Fix double slash in directory urls #355

merged 1 commit into from
Mar 20, 2024

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bjlang
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@bjlang bjlang 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).

@bjlang bjlang requested a review from JoseEspinosa March 20, 2024 09:09
@bjlang bjlang changed the title Fix double slash in directory urls #332 Fix double slash in directory urls Mar 20, 2024
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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 3687239

+| ✅ 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 09:11:16

@bjlang bjlang requested a review from luisas March 20, 2024 11:09
@JoseEspinosa
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Lint will be fixed after template merge

@JoseEspinosa JoseEspinosa merged commit fdc35e7 into nf-core:dev Mar 20, 2024
10 of 11 checks passed
@bjlang bjlang mentioned this pull request Mar 20, 2024
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This was referenced Jul 4, 2024
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@luisas luisas luisas approved these changes

@JoseEspinosa JoseEspinosa Awaiting requested review from JoseEspinosa

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@bjlang @JoseEspinosa @luisas