mag 3.1.0 - Pink Panda

Caution

This release contains a potentially 'breaking change' for some users. The --gtdbtk_pplacer_scratch flag has been replaced with --gtdbtk_pplacer_useram. Check the parameter documentation for more details.

Added

• #665 - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
• #670 - Added --gtdbtk_pplacer_useram to run GTDBTk in memory mode rather than write to disk (requested by @harper357, fixed by @jfy133)

Changed

• #664 - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs)
• #676 - Added exit code 12 to valid SPAdes retry codes, due to OOM errors from spades-hammer (reported by @bawee, fix by @jfy133)

Fixed

• #667 - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133)
• #670 - Re-add missing GTDBTk parameters into GTDBTk module (reported by harper357, fixed by @jfy133)
• #672 - Fix GTDB-Tk per-sample TSV files not being published in output directory (reported by @jhayer, fix by @jfy133)

Dependencies

Tool	Previous version	New version
GTDBTk	2.3.2	2.4.0

Deprecated

• #670 - Deprecated --gtdbtk_pplacer_scratch due to unintuitive usage (reported by harper357, fixed by @jfy133)