Snakemake orchestration for the real-data pipeline - #852

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cailmdaley wants to merge 21 commits into

feat/snakemake-orchestration

Commits on Jul 16, 2026

feat(orchestration): Snakemake workflow for the real-data pipeline (#848)

cailmdaley
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claude
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f92cb44
fix(orchestration): resolve {threads} at rule level, not inside params.cmd

cailmdaley
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187950c
fix(orchestration): carry original exposure names through the index; star-cat store naming

cailmdaley
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ac6bddd
fix(orchestration): exposure-name pass-through, star-cat dirs, P0 run config

cailmdaley
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9b0456e
fix(orchestration): {output} placeholder inside params.cmd survives literally

cailmdaley
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6fe141f
fix(orchestration): shard the exposure forest — the module glob's shape is not cosmetic

cailmdaley
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a110d89
fix(orchestration): carry a wrapper-scripts content hash into every rule's params

cailmdaley
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28c10d8
fix(orchestration): keep snakemake state and index off /project (hard-full quota)

Cail Daley
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a273e76

Commits on Jul 17, 2026

fix(orchestration): drop exp_mask's dead per-unit star-cat input

Cail Daley
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0010def

Commits on Jul 31, 2026

fix(orchestration): nibi-flavor completeness counts; file-level attrition reporting

Cail Daley
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833aa93
feat(ngmix): env-expanded chunk fields; position-seeded RNG becomes the only mode

Cail Daley
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20cc506
feat(orchestration): committed workflow configs — no wrapper, no runtime rewriting (#848 D2)

Cail Daley
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d1c0afb
feat(orchestration): manifests become the DAG's currency — completeness check CLI + manifest-driven report (#848 D2/D3)

cailmdaley
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1b22b98
feat(orchestration): the rules rewrite — manifests as DAG currency, sharded stores, parse-time index, native scattergather (#848 D1–D5)

cailmdaley
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83d26f2
fix(orchestration): harden the rewrite against its adversarial review

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b149e18
feat(orchestration): clean_exposure becomes an in-DAG rule with tombstones (#848 D5, S5)

Cail Daley
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12ecfc2
feat(orchestration): nibi profile goes slurm-executor (#848 D4, S6)

Cail Daley
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e677f67
fix(orchestration): stop the clean_exposure cascade; report reads tombstones (#848 D5)

Cail Daley
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96c78cd
docs(orchestration): profile comment tells the truth about the clean/trigger gate

Cail Daley
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4d28897
run: point the quad at a fresh smk-g3 run dir (old smk-p0 tree is unsharded, pre-manifest)

Cail Daley
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831a127
fix(orchestration): slurm_account is the association name (def-mjhudson_cpu)

Cail Daley
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f82e7f4