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Add MultiQC report #57

Merged
merged 5 commits into from
Jul 3, 2023
Merged

Add MultiQC report #57

merged 5 commits into from
Jul 3, 2023

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grst
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@grst grst commented Jun 29, 2023 •
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Adds FastQC and a basic MultiQC report.

Additional MultiQC modules, such as spaceranger or checkatlas, can be added in follow-up PRs as discussed in #40.

Since we now have MultiQC back in, I could also get rid of the custom diff for dumpsoftwareversions.

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/spatialtranscriptomics 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 Jun 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 08fda75

+| ✅ 154 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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 README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered 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 usage.md: Add documentation section on analysis options/params.
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-29 12:56:19

@fasterius fasterius merged commit 275c895 into nf-core:dev Jul 3, 2023
@grst grst deleted the multiqc branch July 28, 2023 07:58
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@fasterius fasterius fasterius approved these changes

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@grst @fasterius