Batching assemblies throughout workflow - #15

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claudiacarter wants to merge 12 commits into

limit-intermediate-filesfrom

validate-batching

Commits on Aug 29, 2026

Fix construction of SORF EXTRA inputs
claudiacarter
committed
f0aed0a
Ensure bulk annotation and bakta db are value channels
claudiacarter
committed
11d3e95
Use updated bakta fork container - with pseudogenes.py input corrections
claudiacarter
committed
46fc65f
Tag SORF EXTRA
claudiacarter
committed
2d96714
Fix variable interpretation in SORF EXTRA
claudiacarter
committed
f08bb9d
Force bakta to write again to the same dir when used in a loop in SORF EXTRA
claudiacarter
committed
033adfd

Commits on Aug 30, 2026

Unbatch rna and cds pickles in SORF EXTRA + minor formatting changes
claudiacarter
committed
460897f

Commits on Aug 31, 2026

Strip sorf-extra from output gff3 when bundled
claudiacarter
committed
454e9f0