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SamStudio8 / reticulatus

A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads
MIT License
68 stars 5 forks source link

Time and resource logging #3

Closed SamStudio8 closed 4 years ago

SamStudio8 commented 5 years ago

would be nice

SamStudio8 commented 4 years ago

In the first instance this can be done with the benchmark option, but must be added on a per-rule basis. It would be good if we could just encapsulate every rule in the pipeline. Seems this is probably a job for a chitineqsue shell-based solution #6

SamStudio8 commented 4 years ago

Just use the benchmark directive and get over it

SamStudio8 commented 4 years ago

I wanted to use the recent hack of the snakemake shell.py to add time and resource logging with the psutil library, but it turns out that that is pretty much how the snakemake.benchmark module works