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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

Commits on Jan 17, 2022

  1. WIP refactor workflows into subworkflows

    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 committed Jan 17, 2022
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Commits on Jan 20, 2022

  1. Kallisto works again

    grst committed Jan 20, 2022
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Commits on Jan 22, 2022

  1. Finish refactor salmon

    grst committed Jan 22, 2022
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  2. Finish refactoring starsolo

    grst committed Jan 22, 2022
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  3. Fix eclint

    grst committed Jan 22, 2022
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Commits on Jan 26, 2022

  1. Unify multiqc

    grst committed Jan 26, 2022
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Commits on Jan 31, 2022

  1. Make kb_workflow an enum

    grst committed Jan 31, 2022
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