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title: "Bug: pipeio_run doesn't pass --configfile or --directory to snakemake status: resolved created: 2026-03-31 updated: 2026-03-31 timestamp: 20260331-130712-185688 tags: [issue] source: agent-observation project_primary: projio capture_id: 20260331-130710-e3121c confidence: 1.0 transcript_file: /storage2/arash/worklog/workflow/captures/20260331-130710-e3121c/transcript.txt

Bug: pipeio_run doesn't pass --configfile or --directory to snakemake

pipeio_run now correctly uses conda run but doesn't pass --configfile or --directory. The Snakefile has configfile: "config.yml" which resolves relative to --directory (defaults to cwd, which is the project root). Need to either: - Pass --configfile code/pipelines/{pipe}/{flow}/config.yml, or - Pass --directory code/pipelines/{pipe}/{flow}/

Error: WorkflowError: Workflow defines configfile config.yml but it is not present or accessible (full checked path: /storage2/arash/projects/pixecog/config.yml)

The previous manual dry-run worked because we passed both --snakefile and --configfile explicitly.

Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits: 

6c3f258 batch task 1/3: Create new pipeline: coupling (spindle-ripple cross-correlograms)
3f3bea6 batch tasks 1-3/3: Create coupling pipeline with cross-correlogram, spatial coupling, and report mods
47aa65f batch task 5/5: Add QC visualization mod to spectrogram/burst pipeline

README:

type: readme

Quick Start for Collaborators

Follow this checklist to get started with Pixecog documentation and workflows.

🐀 Pixecog Project — Compact Overview

Core principles

  • One immutable BIDS raw dataset (raw/) as the canonical baseline
  • Each analysis pipeline ha
  • [[issue-arash-20260331-125628-712113.md]] — Both are pipeio_run bugs affecting snakemake invocation — conda env and configfile/directory flags are related gaps in the same run wrapper
  • [[issue-arash-20260330-031350-558222.md]] — Also documents pipeio bugs discovered during pipeline mod execution, likely overlapping root causes
  • [[issue-arash-20260330-191230-344783.md]] — Task execution failure that may stem from the same pipeio_run invocation issues
  • [[issue-arash-20260326-232732-019412.md]] — Tracks pipeio implementation work — fixing run invocation is part of completing that feature