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2 Motif Analysis CWL Steps, Neither Used? #59

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SFD5311 opened this issue May 15, 2024 · 0 comments

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SFD5311 commented May 15, 2024

As far as I can tell, neither:
https://github.com/hubmapconsortium/sc-atac-seq-pipeline/blob/develop/steps/motif_analysis.cwl
Nor:
https://github.com/hubmapconsortium/sc-atac-seq-pipeline/blob/develop/steps/motif_and_tf_analysis.cwl
Are used anywhere in the bulk or sc ATACseq pipeline.

If this is the case, we should remove these. If we want to re-introduce chromVAR analysis, we might be able to do it with this package:

https://pychromvar.readthedocs.io/en/latest/api.html

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