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Published 20 hours ago • verified publisher icon nf-core

Added ability to auto-create samplesheet for nf-core/phageannotator

Open CarsonJM opened this issue 2 years ago • 3 comments

PR checklist

  • [X] This comment contains a description of changes (with reason).
  • [X] If you've fixed a bug or added code that should be tested, add tests!
  • [X] 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/mag branch on the nf-core/test-datasets repository.
  • [X] Make sure your code lints (nf-core lint).
  • [X] 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.
  • [x] CHANGELOG.md is updated.
  • [x] README.md is updated (including new tool citations and authors/contributors).

CarsonJM avatar Nov 20 '23 22:11 CarsonJM

nf-core lint overall result: Failed :x:

Posted for pipeline commit 5b37df5

+| ✅ 201 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌  10 tests failed       |-

:x: 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/WorkflowMag.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

:heavy_exclamation_mark: Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • 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_lint - Input mimetype is missing or empty

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-30 20:21:42

github-actions[bot] avatar Nov 20 '23 22:11 github-actions[bot]

@nf-core-bot fix linting

CarsonJM avatar Jan 17 '24 23:01 CarsonJM

Regarding your questions:

  1. I think it would be a good idea to create an umbrella workflow for generating samplesheets for any downstream nf-core pipeline
  2. Great suggestion, I will make that change
  3. It is possible that they would want to keep them separate, so I can make that an option!

CarsonJM avatar Feb 09 '24 16:02 CarsonJM