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Add documentation #49

Merged
merged 16 commits into from
Nov 2, 2023
Merged

Add documentation #49

merged 16 commits into from
Nov 2, 2023

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Lucpen
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@Lucpen Lucpen commented Nov 1, 2023

PR checklist

  • Added required documentation
  • 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
  • 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).

@Lucpen Lucpen requested a review from jemten as a code owner November 1, 2023 13:19
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github-actions bot commented Nov 1, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit af9d576

+| ✅ 130 tests passed       |+
#| ❔ 258 tests were ignored |#
!| ❗  11 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 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in tomte.nf: change this to use the plugin nf-validation
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/genomic-medicine-sweden/tomte/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/nf-core/tomte/master/nextflow_schema.json

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-02 09:01:02

lucia.pena.perez@scilifelab.se added 2 commits November 1, 2023 14:22
@Lucpen Lucpen linked an issue Nov 1, 2023 that may be closed by this pull request
Document the pipeline #41
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@Lucpen Lucpen added documentation Improvements or additions to documentation Ready for review Ready for review labels Nov 1, 2023
jemten
jemten reviewed Nov 1, 2023
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Massive work @Lucpen!
Some comments and suggestions

README.md Outdated Show resolved Hide resolved
README.md Outdated Show resolved Hide resolved
README.md Outdated Show resolved Hide resolved
bin/drop_filter_results.py Show resolved Hide resolved
docs/usage.md Outdated Show resolved Hide resolved
docs/output.md Outdated Show resolved Hide resolved
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Lucpen and others added 4 commits November 1, 2023 20:19
@Lucpen @jemten
Apply suggestions from code review
d9885e0 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
@Lucpen @jemten
Update docs/usage.md
2a9dc98 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
fix by running prettier
1027ac3
fix by running prettier
af9d576
jemten
jemten approved these changes Nov 2, 2023
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🎅 👍

@Lucpen Lucpen merged commit 0ab47a2 into master Nov 2, 2023
7 checks passed
@Lucpen Lucpen deleted the add_documentation branch November 2, 2023 09:52
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Document the pipeline
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