v0.9.0

Upgrading to v0.9.0

There are several significant changes to output files from v0.8.4 that will affect downstream processing. Upgrading may also require rerunning existing analyses because filenames have changed. Please see genome-grist#225 for a summary guide to upgrading to v0.9.0 from v0.8.4.

Details

Significant new features:

• remove abundance trimming from the default genome-grist workflow (#199)
• change column names in mapping summary files; add count of mapped reads. (#209, #219)

Other changes::

• fix calculation of memory required for prefetch step (#229)
• fix trim-low-abund ksize to match sourmash db ksize (#218)
• Allow everything but hyphens and periods in sample names (#188)
• switch to gzipped sourmash input/output files (#213)
• add an initial summary of output files and their contents (#211)
• fix notebook to properly handle a single mapping result (#214)
• Speed up copy_local_genomes.py with symbolic links (#181)
• fix returncode (#200)
• provide a better error message for empty prefetch; upgrade sourmash versions (#195)
• fix genome download rule (#233)

Full Changelog: v0.8.4...v0.9.0