Batch per-genome processes - #13

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flass wants to merge 44 commits into

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limit-intermediate-files

Commits on Aug 6, 2026

Batch input files and record metadata
claudiacarter
committed
7f6e24c
Adapt CDS search for new metadata and batch logic
claudiacarter
committed
38ee7b6

Commits on Aug 8, 2026

Add set pipefail to error on a within-batch error
claudiacarter
committed
74f2f84
Handle rna and cds channels using meta
claudiacarter
committed
fe34e0c

Commits on Aug 11, 2026

Update merge annotations script to process batched pickles instead of genome specific pickles
claudiacarter
committed
247ff4f
Add script capable of batching and unbatching Bakta pickle outputs - to supercede merge_pickles.py
claudiacarter
committed
9719f74

Commits on Aug 14, 2026

differentiate buffer sizes based on task execution times
flass
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01794d7
remove redundant set pipefail
flass
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06fd292
add batching and pulishing logic
flass
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c52e414
adapt RNA wf
flass
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c354095
Revert "differentiate buffer sizes based on task execution times"
flass
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4e3d54a
finish adapting merge_annotation to batches
flass
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53b3dcb

Commits on Aug 17, 2026

use manage_pkls.py
flass
committed
dfd2d4d

Commits on Aug 18, 2026

further into wf
flass
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68f436a

Commits on Aug 19, 2026

updated bakta container for testing
flass
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b6426de

Commits on Aug 20, 2026

simplify workflow structure and syntax
flass
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ee43af3
add meta throughout for channel joining
flass
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9f1e74b
use manage_pkls.py
flass
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cb88ded

Commits on Aug 21, 2026

joinng of channels using meta.tag
flass
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1932564
use explicit argument params.mmseqs_clustering != "strict" to command use of EXTEND_ANNOTATIONS
flass
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f9d41e9
dispatch output into separate folders
flass
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9a86d61
refactor generate aux db and make it use batched input
flass
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e767a18
disambiguate gff3 output channels
flass
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d2de36b
debug config
flass
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dade34d

Commits on Aug 22, 2026

toInteger
flass
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046e42e
cast str to int
flass
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d9fd5e2

Commits on Aug 23, 2026

skip problematic conditional statement
flass
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cf0a161
typo
flass
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6613e97
clean input syntax
flass
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179906e
clean publishDir syntax
flass
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228da8a
separate input channels
flass
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68800b6
correct ch name
flass
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7250d26
move sampleIdFromName function to subwf
flass
committed
57af7f3

Commits on Aug 24, 2026

Commits on Aug 25, 2026

chmod +x bin/manage_pkls.py
flass
committed
e488b64
fix config selector for DETECT_PSEUDOGENES
flass
committed
38d39e5

Commits on Aug 26, 2026