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Merged
Parent: Release 1.1.0 - Resolution Road
merged 12 commits into from
Nov 14, 2023
Merged

Documentation #19

merged 12 commits into from
Nov 14, 2023

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@kbestak
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@kbestak kbestak commented Nov 10, 2023

Added documentation and updated nf-core module versions.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • 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).

Missing CITATIONS and README still

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github-actions bot commented Nov 10, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e88a4c3

+| ✅ 158 tests passed       |+
!| ❗  12 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-14 10:58:20

@kbestak
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kbestak commented Nov 13, 2023

Added mentioned citations and readme^^

@kbestak kbestak self-assigned this Nov 13, 2023
@FloWuenne
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LGTM! Next step, nf-test 🚀!

@FloWuenne FloWuenne merged commit 3c46f9d into dev Nov 14, 2023
@FloWuenne FloWuenne deleted the Documentation branch November 14, 2023 11:46
@kbestak kbestak mentioned this pull request Nov 14, 2023
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@kbestak @FloWuenne