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Submit tasks as job arrays and fix RNAs in distill summaries #472

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976c683
updated config files, added array size parameter for cluster execution
tpall Nov 20, 2025
ef13eed
updated nextflow.config
tpall Nov 20, 2025
d9a3bc6
Swap output assignments for rRNA and tRNA collections
tpall Nov 21, 2025
a087cf4
Merge branch 'dev' of https://github.com/WrightonLabCSU/DRAM into dev
tpall Nov 21, 2025
f5697b2
Merge branch 'dev' of https://github.com/tpall/DRAM into dev
tpall Nov 21, 2025
63ea268
Refactor distill script and configuration for improved clarity and fu…
tpall Nov 25, 2025
7414979
Refactor input and output path definitions for consistency in the SUM…
tpall Nov 26, 2025
a77c29e
Fix conditional check for gene columns in genome summary export to pr…
tpall Nov 26, 2025
e8b0e95
Refactor channel usage for consistency across workflows and improve r…
tpall Nov 26, 2025
4418739
Update SUMMARIZE module to use parameterized fasta column for grouping
tpall Nov 27, 2025
cd3b7ac
Fix closure in QC workflow
tpall Nov 28, 2025
ed054bd
Fix closure in DB_SEARCH workflow
tpall Nov 28, 2025
d39ff14
Updated combine_annotations.py to fix binwise summary. TODO: getting…
tpall Dec 1, 2025
64ab39e
Add QC:COLLECT_RNA to array pattern
tpall Dec 18, 2025
1ee2aea
Merge branch 'dev' of https://github.com/WrightonLabCSU/DRAM into dev
tpall Dec 23, 2025
2c93e2a
Merge branch 'dev' of https://github.com/WrightonLabCSU/DRAM into dev
tpall Dec 23, 2025
702666f
Merge branch 'dev' of https://github.com/tpall/DRAM into dev
tpall Dec 23, 2025
69b23f2
Merge branch 'dev' of https://github.com/WrightonLabCSU/DRAM into dev
tpall Mar 3, 2026
23b1a18
feat: accept gzip-compressed fasta input
tpall Apr 24, 2026
3059c89
fix: register array_size in schema so it validates
tpall Apr 24, 2026
d00f417
chore: remove unused trees subsystem and DRAM-v1 legacy setup scripts
tpall Apr 24, 2026
8c7dcf8
chore: remove DRAM-v1 db_description_builder and db_utils
tpall Apr 24, 2026
721fcaa
fix(db_search): correct DB_channel_SETUP case mismatch
tpall Apr 25, 2026
f1a60ec
fix(db_search): correct formattedOutputchannels case mismatch
tpall Apr 25, 2026
051d70b
fix(annotate): drop MMSEQS_INDEX publishDir to save disk
tpall Apr 26, 2026
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86 changes: 0 additions & 86 deletions assets/internal/generate_sql_database.py
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