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Refactor workflows into subworkflows #87

Merged
merged 8 commits into from
Jan 31, 2022
Merged

Refactor workflows into subworkflows #87

merged 8 commits into from
Jan 31, 2022

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grst
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@grst grst commented Jan 17, 2022 •
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There are already some redunancies between the different
"workflows" (salmon/alevin/star). This will be getting
worse as additional features downstream of the quantification
are getting implemented (e.g. conversion to AnnData, ambient
RNA filtering etc.)

This is the beginning of a series of commits that will
turn the workflows into subworkflows:

  • Streamline parameter validation and move to main workflow
  • Make the different alignment workflow subworkflows that are
    independent of params and get all input values via take instead
  • Make cellranger subworkflow available -> separate PR

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated. -> didn't update as it's not a change related to a previous version of the pipeline (still part of porting it to DSL2)
  • README.md is updated (including new tool citations and authors/contributors).

@grst
WIP refactor workflows into subworkflows
f0f2963 
There are already some redunancies between the different
"workflows" (salmon/alevin/star). This will be getting
worse as additional features downstream of the quantification
are getting implemented (e.g. conversion to AnnData, ambient
RNA filtering etc.)

This is the beginning of a series of commits that will
turn the workflows into subworkflows:
 - [ ] Streamline parameter validation and move to main workflow
 - [ ] Make the different alignment workflow subworkflows that are
       independent of `params` and get all input values via `take` instead
 - [ ] Make cellranger subworkflow available
@grst grst marked this pull request as draft January 17, 2022 21:19
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github-actions bot commented Jan 26, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4f46e48

+| ✅ 140 tests passed       |+
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_description - Ungrouped param in schema: skip_multiqc
  • schema_description - Ungrouped param in schema: seq_center
  • schema_description - No description provided in schema for parameter: protocol
  • schema_description - No description provided in schema for parameter: star_ignore_sjdbgtf

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-01-31 09:53:45

@grst grst marked this pull request as ready for review January 26, 2022 13:23
@grst grst mentioned this pull request Jan 26, 2022
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@grst grst requested a review from apeltzer January 26, 2022 16:20
ggabernet
ggabernet approved these changes Jan 26, 2022
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Looks good to me, it simplifies quite a bit of the parameter logic

nextflow_schema.json Show resolved Hide resolved
@grst grst merged commit c8d04dc into nf-core:dev Jan 31, 2022
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@ggabernet ggabernet ggabernet approved these changes

@apeltzer apeltzer Awaiting requested review from apeltzer

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