Metagenome-atlas

Latest version: v2.0.0

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* bug fixes where assembly was only using SE reads
* updates to checkm where databases are now downloaded separately

+ bug fixes
+ adds read length stats
+ makes deduplication (via `clumpify.sh`) default

+ adds new pre-processing protocols

+ updates environment to pinned versions

+ updates annotation protocol
+ adds checkm bin annotation

+ fixes file path report when checking config file to improve "config file is invalid" message

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