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Fix for pipeio_run --directory issue: cd into flow directory before launching snakemake

Simpler than passing --configfile: pipeio_run should set the working directory to the flow directory (code/pipelines/{pipe}/{flow}/) before launching snakemake in the screen session. This matches how the flow Makefile works — it runs from its own directory.

This supersedes the previous issue (20260331-130712) about missing --configfile. The fix is: cd {flow_dir} && conda run -n {env} snakemake ... in the screen command.

Alternatively, pipeio_run could just invoke the flow Makefile targets directly (e.g. make run MOD=ttl_removal) which already handles all path resolution.

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

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  • [[issue-arash-20260331-130712-185688.md]] — Direct predecessor issue about missing --configfile/--directory in pipeio_run that this fix supersedes
  • [[issue-arash-20260331-125628-712113.md]] — Related pipeio_run execution issue (conda env not activated), same component and likely same run session
  • [[issue-arash-20260330-031350-558222.md]] — Earlier pipeio bugs discovered during ttl_removal mod creation, likely overlapping context