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New rules for generating subsets of bigWig files#196

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cnluzon merged 5 commits intomainfrom
rules
Jun 27, 2025
Merged

New rules for generating subsets of bigWig files#196
cnluzon merged 5 commits intomainfrom
rules

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@cnluzon cnluzon commented Jun 3, 2025

This PR adds ways to reduce the amount of bigWig files generated to the minimal set of meaningful ones. The idea is that most of the time we don't need to produce both scaled and unscaled files, so now there are rules to produce scaled treatments and unscaled (RPGC-scaled) controls, generally halving the amount of bigWig files generated. More specifically:

  • quick: This rule existed previously, as opposed to full which also runs the fingerprints, but now it also includes only the minimal set of bigwigs. It is not currently the default, although I am considering making it the default final rule.
  • pooled_only_minimal: Pooled replicates in groups.tsv but only scaled for treatments and unscaled for controls.

I have also included a get_all_controls function and now treatments and controls exist as global variables for legibility of these sets.

@cnluzon cnluzon merged commit 9a339a3 into main Jun 27, 2025
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@cnluzon cnluzon deleted the rules branch June 27, 2025 08:35
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