Closed uzbit closed 10 months ago
Hey @uzbit,
that seems more like a request for snakemake in general, rather than for grenepipe in particular :-)
Snakemake offers the --printshellcmds
, which might do what you want. Let me know if that helps. If not, I'd suggest to open an issue over on their GitHub repo.
Cheers Lucas
That was it! thanks!
Awesome, that was easy to solve ;-)
Perhaps this already exists and I haven't found it yet, but it would be really helpful for tuning and debugging a pipeline if we could see the individual commands at each step.
For example, all of the log/mpileup/*.log files are empty, which i guess means there was no output from the command, but ideally this should contain the command executed too.
Thanks!