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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
MIT License
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[Question] where to find the exact command issued? #1012

Closed sunta3iouxos closed 2 months ago

sunta3iouxos commented 2 months ago

Hi all, Where can I find the commands issued for each step of the analysis? I do not see them in any log file and apparently the sbatch commands are deleted (?). Thank you

katsikora commented 2 months ago

Hi,

if you run the workflow with --verbose, it will be logged to the main log in the output folder. Otherwise, some of the commands get logged into the *.err files in the cluster_logs folder upon error, assuming you're running snakePipes on a cluster.

Best wishes,

Katarzyna

sunta3iouxos commented 2 months ago

Perfect, Thank you