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Published 20 hours ago • verified publisher icon nf-core

addition of emptyDrops draftdownstream modules

Open rlinchangco opened this issue 1 year ago • 2 comments

This is a draft for adding emptyDrops functionality to the pipeline, using a python ported implementation of the R package: https://github.com/nh3/emptydrops

New additions include: empty_drops.nf empty_drops_filter.nf filter_by_emptydrops.py

The two things that definitely still need work are in empty_drops_filter.nf is to check the inputs to be sure it's the data directory path, and to add an output directory path

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/scrnaseq 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).

rlinchangco avatar Oct 05 '22 13:10 rlinchangco

@fmalmeida Here is the draft we disscussed!

rlinchangco avatar Oct 05 '22 13:10 rlinchangco

nf-core lint overall result: Passed :white_check_mark:

Posted for pipeline commit ae8fb07

+| ✅ 158 tests passed       |+

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-09 14:54:47

github-actions[bot] avatar Oct 05 '22 13:10 github-actions[bot]

Hi @rlinchangco, I am planning to help you on this one. Can you add me as a contributor to your fork so I can commit to it and help on the PR?

fmalmeida avatar Nov 09 '22 11:11 fmalmeida

General question, what's the plan for the implementation?

EMPTYDROPS_FILTER should come right before matrices conversion and concatenation? Shall it be always on? Or have a params.filter_emptydrops parameter for it?

fmalmeida avatar Nov 09 '22 14:11 fmalmeida

@nf-core-bot fix linting

fmalmeida avatar Nov 09 '22 14:11 fmalmeida

The script expects a parameter called --version which is defined like this:

parser.add_argument(
        "-v",
        "--version",
        dest="version",
        default=3,
        help="Version for features file, defines expected file name (1=kallisto,<v3 cellranger,3=star,>=v3 cellranger).",
    )

I could actually not understand what it expects. It would not work for salmon/alevin? Guess to make it easier to use values already defined on parameters and meta.maps, instead of having a different definition, may this option ask for the aligner name directly? Or the actual protocol?

fmalmeida avatar Nov 09 '22 14:11 fmalmeida