Pnnl-atlas

Latest version: v1.0.32

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+ adds reports to python package

* fixes bug in command line for featureCounts
* fixes bug when using `atlas annotate` without fastqs

* 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

Has known vulnerabilities