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feat: collapse peak p-values in bedtools/merge, reformat with new process #39

Merged
merged 27 commits into from
Dec 1, 2023
Merged

feat: collapse peak p-values in bedtools/merge, reformat with new process #39

merged 27 commits into from
Dec 1, 2023

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@kelly-sovacool kelly-sovacool commented Dec 1, 2023 •
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Changes

  • new process formatmergedbed to take the output from calling bedtools merge -c 1,5,6,7,8,9 -o count,collapse,collapse,collapse,collapse,collapse on concatenated peak files and format it as a narrow peak file.
    • For each consensus peak, the score/p-value/q-value etc. is kept for the peak with the highest -log10(p-value).
  • Peak p-values are normalized prior to bedtools merge.
  • Bedtools merge now accepts optional CLI args as a second input channel.
  • Now use GNU sort instead of bedtools sort -- more efficient per bedtools docs.

Issues

Related to CCBR/CHAMPAGNE#151

PR Checklist

(Strikethrough any points that are not applicable.)

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • Write unit tests for any new features, bug fixes, or other code changes.
  • Update docs if there are any API changes.
  • Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

@kelly-sovacool
refactor: normalize peaks individually before merge
acf72da
@kelly-sovacool
refactor: accept CLI args as channel
f7dd94c
@kelly-sovacool
refactor: use bed basename for outfile
b21c698
@kelly-sovacool
chore: include code from older normalizepeaks process
3e600f3
@kelly-sovacool
feat: new process formatmergedbed to finalize consensus peak file
79a9c28
@kelly-sovacool
chore: ignore RStudio-related files
4e3d970
@kelly-sovacool
test: bedtools/merge now accepts optional args
59a2eb4
@kelly-sovacool
test: run tests for formatmergedbed
6ce2851
@kelly-sovacool
refactor!: use formatmergedbed in consensus_peaks
0f78545
@kelly-sovacool
chore: update changelog
f667941
@kelly-sovacool
chore: remove unneeded imports
beca2ea
@kelly-sovacool
refactor: use input baseName as default output prefix
d343681
@kelly-sovacool
feat: new process sort/bed
a6119b2 
uses GNU sort on bed file.
more efficient than bedtools sort.
https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
@kelly-sovacool
refactor: use sort/bed instead of bedtools/sort
c0162ab
@kelly-sovacool
refactor: use sort/bed instead of bedtools/sort in test
d98743f
@kelly-sovacool
fix: sort input files for reproducibility
0874c77
@kelly-sovacool
refactor: use sort/bed instead of bedtools/sort for consensus_peaks
4c3c721
@kelly-sovacool
fix: sort on file basename before collecting
8e65ce1
@kelly-sovacool
fix: make sure ties are not kept in slice_max
440a01d
@kelly-sovacool
fix: use full peak filename
2e86b88 
preserve narrowPeak vs broadPeak
@kelly-sovacool
test: update consensus_peaks with sort/bed module
629f8e3
@kelly-sovacool kelly-sovacool self-assigned this Dec 1, 2023
@kelly-sovacool kelly-sovacool merged commit d1cb7d8 into main Dec 1, 2023
21 of 23 checks passed
@kelly-sovacool kelly-sovacool deleted the cons-peak-norm branch December 1, 2023 21:37
@kelly-sovacool kelly-sovacool added this to the 2023w48_1201 milestone Jan 10, 2024
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