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Documentation #63

Merged
merged 14 commits into from
Jan 4, 2024
Merged

Documentation #63

merged 14 commits into from
Jan 4, 2024

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fasterius
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PR checklist

This PR adds various documentation changes, as well streamlining some parameters and removing unused ones.

  • This comment contains a description of changes (with reason).
  • 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.
  • README.md is updated (including new tool citations and authors/contributors).

@fasterius fasterius self-assigned this Jan 4, 2024
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github-actions bot commented Jan 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0fe89c8

+| ✅ 158 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • 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 output.md: More details for each analytical step should probably be added,
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-04 17:14:57

@fasterius fasterius marked this pull request as ready for review January 4, 2024 17:22
@fasterius fasterius merged commit 5657ec7 into dev Jan 4, 2024
8 checks passed
@fasterius fasterius deleted the documentation branch January 4, 2024 17:23
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