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Output improvements#191

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AroneyS merged 22 commits intomasterfrom
output-improvements
Sep 22, 2025
Merged

Output improvements#191
AroneyS merged 22 commits intomasterfrom
output-improvements

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@AroneyS AroneyS commented Sep 3, 2025 •
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  • Log # of coassemblies found of each size
  • Genome extraction:
    • Apply iterate bin extraction at the end of coassemble when run with run-aviary
    • Extract all Aviary bins to folder, renamed numerically from binchicken + coassembly name
    • Include a compiled quality report, bin info using the new names
    • Create provenance file with name conversion
    • Account for bin_info with different col types
    • Add details to logging
  • Use recovered_bins for evaluate and iterate
  • Add to docs
  • Test run demo

AroneyS added 22 commits September 3, 2025 14:05
@AroneyS
add more logging to output
839c906
@AroneyS
add check that elusive clusters exists before loading
02e2399
@AroneyS
add bin extraction after coassemble
57ee552
@AroneyS
collate bin_info and quality_report
9a2dd1e
@AroneyS
move bin extraction to its own function
442bd17
@AroneyS
check for data in bin_infos before concat
1e848f6
@AroneyS
change output to recovered/bins with tsvs in main dir
ce66d5f
@AroneyS
change evaluate and iterate to use genomes in recovered dir when avai…
5e3a886 
…lable
@AroneyS
fix ext being removed
2f1a3ea
@AroneyS
update setup
48d148a
@AroneyS
add more details to databases
4589d41
@AroneyS
add --dry-run as another option
5e155f2
@AroneyS
more docs improvements
53ae8f6
@AroneyS
fix tmpdir being considered for downloading
72e1d1d
@AroneyS
remove incorrect update arg verification
dee3e4d
@AroneyS
add check_binchicken_completion.py script to extras
599713b
@AroneyS
fix bin_info schema
07f1cc9
@AroneyS
remove groups from all rules
dc276fd 
snakemake can't handle grouped jobs with different resources (log_path)
@AroneyS
fix test
14d9e87
@AroneyS
rename iterate bin provenance file
9f80512
@AroneyS
fix tests
ffa5276
@AroneyS
fix tests properly
9ea66a9
@AroneyS AroneyS merged commit 9635086 into master Sep 22, 2025
5 of 6 checks passed
@AroneyS AroneyS deleted the output-improvements branch September 22, 2025 00:33
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@AroneyS