CODEWITHSUNDEEP
snakemake
sebio
sebio

Reputation: 138

Snakemake: Wrapper command logging

I fail to figure out how I can log the commands executed by a wrapper. Both "snakemake -p" and "snakemake -D" are not showing me the actual commands that were run.

What is the best approach for logging the commands created through a wrapper?

Cheers, Seb

Upvotes: 2

Views: 323

Answers (1)

Johannes Köster
Johannes Köster

Reputation: 1927

So, currently, -p is indeed not propagated to scripts or wrappers. However, I have just changed that in the code, and the upcoming release 4.0 will give you what you want with snakemake -p.

Note that wrappers often do more than executing a single shell command. You can find the entire source code of a wrapper on the respective page in the wrapper description. E.g., see here for bwa mem: https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/bwa/mem.html#code

Upvotes: 1

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