v2.0.0: pyrodigal-gv gene caller, ProstT5+Foldseek structural phage detection, open-source MFD solver, direct CoverM, Snakemake 8+ - #68

Merged

Vini2 merged 46 commits into

Vini2:developfrom

gbouras13:feature/prostt5-foldseek-detection

Aug 12, 2026

Commits on Aug 3, 2026

Add pyrodigal-gv as an optional gene caller, selected via --genecaller

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f7a5046
Replace Gurobi with flowpaths (HiGHS-backed) in the MFD solver

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a1f6aaf
Merge branch 'feature/highs-solver' into feature/prostt5-foldseek-detection
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faf006f
Add ProstT5 -> Foldseek structural phage-gene detection, selected via --phagedetection

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77b44ba
Add GPU backend selection for ProstT5/foldseek, container support, relax Python pin

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acd2f14
Remove the numpy<2.0.0 pin and the Python <3.13 upper bound

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274fd1b
Migrate to Snakemake 8+ and fix a resource conflict it exposes

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e2531f3
Merge branch 'chore/snakemake8-migration' into feature/prostt5-foldseek-detection
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3126b70
Fix the same mem/mem_mb resource conflict in this branch's own new rules

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3517992
Update bundled phrog_annot.tsv to the accurate PHROG category assignments

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b02ebfc
Merge branch 'fix/update-phrog-annotations' into feature/prostt5-foldseek-detection
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b6505e1
Merge branch 'fix/smg-exclusion-order-dependence' into feature/prostt5-foldseek-detection
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9d6a0a3
Add an optional SLURM GPU-routing profile for predict_3di/scan_hallmark

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e05614c

Commits on Aug 4, 2026

Commits on Aug 5, 2026

Commits on Aug 10, 2026

Work around broken torchaudio in ROCm container (missing libomp.so)
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afe38c5
Fix torchaudio stub: give it a real ModuleSpec, not a bare ModuleType
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86b8c17
Pin prostt5-rocm.yaml to torch==2.7.1+rocm6.3, broaden torchaudio workaround
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c412f41
Replace koverage wrapper with direct CoverM invocation (PLAN.md §4.8)

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a1ac8fd
Document koverage_tsv column layout, add regression test

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6fa8f21
Branch coverm_map's minimap2 preset on config[longreads]

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32bf598
Fix coverm.yaml solver conflict: drop redundant minimap2/samtools pins

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7a3f9f6
Fix coverm_map: samtools view needs -b, defaults to SAM text otherwise

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afcb9b2

Commits on Aug 11, 2026

Finish koverage removal: convert postprocess to direct CoverM, drop koverage

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0ecc830
Bump version to 2.0.0

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0adfe97
Fix CI: stale Python matrix, missing test-time deps

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c919fd3
Add build_hallmark_db.py + docs (closes a promise the CLI already made)

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430f9ab
build_hallmark_db.py: fix missing _ca suffix

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2fd2829
Wire hallmark_db into `phables install` as a pre-built download

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5935cd1
hallmark_db: set real Zenodo URL, drop dereference guidance

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66924b1
docs/usage.md: document the entire fork CLI surface

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98aa263

Commits on Aug 12, 2026

Replace stale pre-fork Dockerfile with a working ROCm/Setonix build + CI

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6942bbc
Add --container: workflow-wide container, replacing conda for every rule

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6a2a501
container: drop cogent3/piqtree, not used in this workflow
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3a38d2d