pipeio_run passes unrecognized --filter-* flags to snakemake¶
When calling pipeio_run(flow="preprocess_ieeg", dryrun=True, wildcards={"subject": "01", "session": "04"}), the tool generates:
snakemake ... --filter-subject 01 --filter-session 04
Snakemake (at least the version installed here) does not recognize --filter-subject / --filter-session:
snakemake: error: unrecognized arguments: --filter-subject --filter-session 04
Wildcard filtering should use snakemake's native target-based scoping or --config overrides instead.
Source context: pixecog¶
PixEcog (pixecog): Neuropixels and ECoG dataset and analysis
Recent commits:
8dc0d9d Pipeline docs: gitignore docs/pipelines/, relocate hand-authored files
96cd1ec Refactor sharpwaveripple/contracts: extract generic helpers to utils/io, remove pipelines __init__.py
36f9326 Add result note directory and sample note
README:
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Related Notes¶
- issue-arash-20260409-232102-577698.md — Both are pipeio_run / pipeio_run_status bugs observed in the same session; likely share the same PipelineContext invocation path
- issue-arash-20260407-050947-246557.md — Covers pipeio fixes including input stage resolution in PipelineContext — the same layer responsible for translating wildcards into snakemake arguments
- issue-arash-20260409-232034-115590.md — Another pipeio tool (pipeio_nb_exec) with incorrect environment/argument handling — pattern of pipeio tools mishandling execution context