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moiexpositoalonsolab / grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
http://grene-net.org
GNU General Public License v3.0
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Write full executed command for each step to log files for reproducibility #38

Closed uzbit closed 10 months ago

uzbit commented 10 months ago

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!

lczech commented 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

uzbit commented 10 months ago

That was it! thanks!

lczech commented 10 months ago

Awesome, that was easy to solve ;-)