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Feature Select Implementation to CytoPipe #6

Merged
merged 10 commits into from
May 13, 2022
Merged

Feature Select Implementation to CytoPipe #6

merged 10 commits into from
May 13, 2022

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axiomcura
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Hello @gwaygenomics

This PR focuses on the feature select implementation. The new files created in this PR are:

  • consensus.py
  • feature_select.py
  • feature_select.smk

@axiomcura axiomcura added the enhancement New feature or request label May 9, 2022
@axiomcura axiomcura requested a review from gwaybio May 9, 2022 18:33
gwaybio
gwaybio approved these changes May 11, 2022
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A couple minor comments. Once you address them all, feel free to merge!

configs/analysis_configs/feature_select_configs.yaml Outdated Show resolved Hide resolved
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rules/feature_select.smk

rule create_consensus:
input:
expand(
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warning: beyond scope of this PR

sometimes we want to create consensus profiles from more than just feature selected files.

We may also want to perform feature selection on all profiles (instead of just by plate).

How would this work? (we can discuss later too, but just something to keep in mind)

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@axiomcura axiomcura May 13, 2022 •
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Wrote it down on my notes ! I'll see what snakemake has to offer!

Based on my current knowledge this, seems this can be done at the configuration level. We can provide a flag indicating the types of consensus we want and the script can handle it.

In addition, I feel that the consensus step is general enough to create a modular function and call it when we are generating different consensus files.

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@axiomcura axiomcura merged commit 638009d into WayScience:main May 13, 2022
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@axiomcura @gwaybio