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Preparing template merge 2.13 #344

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Preparing template merge 2.13 #344

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jasmezz
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@jasmezz jasmezz commented Feb 28, 2024

This prepares the funcscan dev branch for the template merge PR from nf-core-bot (2.13).
Specifically (basically followed Harshil's to-do list in the blog post):

  • installed 3 utils* subworkflows
  • copied all customized functions from lib/WorkflowFuncscan.groovy to subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf
  • deleted lib/ directory
  • outcommented everything in pipeline code that refers to the lib dir files
  • added include statements in the respective main.nfs

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/funcscan 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).

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github-actions bot commented Feb 28, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 778c29f

+| ✅ 217 tests passed       |+
!| ❗   2 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • 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
  • schema_params - Default value for param fasta invalid: Not in pipeline parameters. Check nextflow.config.

❗ 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
  • schema_params - Schema param fasta not found from nextflow config

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-28 15:14:45

@jasmezz
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jasmezz commented Mar 13, 2024

Obsolete, solved by #345

@jasmezz jasmezz closed this Mar 13, 2024
@jasmezz jasmezz deleted the template-2.13 branch March 13, 2024 22:39
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