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Fix bedtools genomecov deprecation (coverage calculation) #209

Merged
merged 4 commits into from
Jan 6, 2022
Merged

Fix bedtools genomecov deprecation (coverage calculation) #209

merged 4 commits into from
Jan 6, 2022

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evanroyrees
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  • 🐍 🔥 Remove deprecated argument bedtools genomecov command
  • 🐍🍏 Rename entrypoint for clarity: autometa-parse-bed -> autometa-bedtools-genomecov
  • 🍏 🎨 Update parse_bed.nf with updated autometa entrypoint
  • 🐍🔥✅ Remove unneeded param in test_coverage.py
  • 🐍🔥 remove unneeded make_length_table(...) from coverage.py

@evanroyrees
🔥🎨 remove deprecated bedtools.genomecov length argument
a6fca66 
🎨 update coverage script to adhere to updated bedtools.genomecov params
@evanroyrees
🎨 update autometa-parse-bed entrypoint
cafd9de 
🎨🍏 update parse_bed.nf entrypoint to correspond to updated autometa entrypoint
@evanroyrees
✅ remove unneeded param in test for bedtools.genomecov(...)
19b6b11
@evanroyrees evanroyrees mentioned this pull request Dec 21, 2021
Merged
@evanroyrees evanroyrees added nextflow Nextflow related issues/code python Python related issues/code labels Dec 21, 2021
@evanroyrees evanroyrees merged commit 9bfb62f into dev Jan 6, 2022
@evanroyrees evanroyrees deleted the coverage branch January 6, 2022 03:21
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