Fix bedtools genomecov deprecation (coverage calculation)

KwanLab / Autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes

https://autometa.readthedocs.io

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Closed evanroyrees closed 2 years ago

evanroyrees commented 2 years ago

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