Benchmark summariser can't get time spent by medaka_consensus on samtools operations

SamStudio8 / reticulatus

A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads

MIT License

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Benchmark summariser can't get time spent by medaka_consensus on samtools operations #22

Closed SamStudio8 closed 4 years ago

SamStudio8 commented 4 years ago

A large part of the medaka consensus step is spent sorting and merging the alignment from minimap2, particularly for the prom-sized data sets. It would be good to know how long we spend here if we're to report timing benchmarks.

SamStudio8 commented 4 years ago

also indexing

SamStudio8 commented 4 years ago

Just calculate the delta