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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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looper runp looper.pep_config output None --solved #267

Closed miximimi closed 10 months ago

miximimi commented 10 months ago

I am not sure if this is already fixed in the newest version, but when I am running the older vesion of pepatac this following bug appeared:

When running looper runp project_config.yaml, project_pipeline_interface.yaml tries to pass --config {looper.pep_config} to pepatac_collator.py but this is not defined anywhere. What I did was changing this to --config {looper.config_file} and added config_file: {my project_config.yaml path} into the looper section of project_config.yaml, and do the rerun. Now this config yaml can be correctly passed to the .py and .R scripts.

If this is already solved in the newest version, feel free to ignore or delete this trend.

Thank you!

donaldcampbelljr commented 10 months ago

Hey, thanks for posting. The preferred way to run everything with the newest changes: looper run --looper-config /your/path/.looper_config.yaml and looper runp --looper-config /your/path/.looper_config.yaml

For a specific example from the tutorial (in pepatac/tutorial/examples): looper run --looper-config .looper_tutorial_refgenie.yaml

Further reading (this affects Looper 1.5.0 and greater): https://looper.databio.org/en/latest/looper-config/ https://github.com/pepkit/hello_looper

donaldcampbelljr commented 10 months ago

Since this is solved, I will close.