Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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 tofullwhich 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 defaultfinalrule.pooled_only_minimal: Pooled replicates in groups.tsv but only scaled for treatments and unscaled for controls.I have also included a
get_all_controlsfunction and nowtreatmentsandcontrolsexist as global variables for legibility of these sets.