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Add MT percentage filtering #97

Merged
merged 9 commits into from
Sep 25, 2024
Merged

Add MT percentage filtering #97

merged 9 commits into from
Sep 25, 2024

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tbrittoborges
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@tbrittoborges tbrittoborges commented Sep 20, 2024 •
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This PR adds support to mitochondrial fraction filtering per sample, a widely used quality metric in snRNAseq.

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/scdownstream 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@tbrittoborges tbrittoborges marked this pull request as ready for review September 20, 2024 09:15
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Closes #87

@nictru nictru linked an issue Sep 20, 2024 that may be closed by this pull request
Add MT percentage filtering #87
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nictru commented Sep 20, 2024

Hey, a couple of small things:

  1. Make sure there are no conflicts with the dev branch (rebase/merge)
  2. As far as I can tell, scanpy gives you a percentage (0-100) while the new pipeline parameter is a fraction (0-1). I might be wrong, did not test. I would prefer to change the pipeline parameter to a percentage in this case (integer between 0 and 100).
  3. Please add a max_ prefix to the column name in the samplesheet. I know only the maximum makes sense here, but for consistency with other thresholds I think it makes sense.

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tbrittoborges commented Sep 24, 2024 •
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1. Make sure there are no conflicts with the `dev` branch (`rebase`/`merge`)

Resolved the merge conflicts on assets/schema_input.json and docs/usage.md.

2. As far as I can tell, scanpy gives you a percentage (0-100) while the new pipeline parameter is a fraction (0-1). I might be wrong, did not test. I would prefer to change the pipeline parameter to a percentage in this case (integer between 0 and 100).

Changed from float to int.

3. Please add a `max_` prefix to the column name in the samplesheet. I know only the maximum makes sense here, but for consistency with other thresholds I think it makes sense.

Added the max prefix.

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github-actions bot commented Sep 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 456d47e

+| ✅ 218 tests passed       |+
!| ❗  13 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 nextflow.config: Specify your pipeline's command line flags
  • 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 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-25 13:18:07

nictru
nictru approved these changes Sep 25, 2024
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@nictru nictru merged commit 7c5d731 into nf-core:dev Sep 25, 2024
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Add MT percentage filtering
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