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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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Benchmark with the vanilla `mtbseq` tool to document run-time #30

Closed abhi18av closed 2 years ago

abhi18av commented 3 years ago

Interesting results:

We need to benchmark the tool for judging how similar are the results for capturing the effects of

  1. Rerunning the analysis on the same platforms (conda / docker (via k8s)) with same cpu/memory settings.

conda (2cpu/8gb) - two times (conda vs conda) k8s/docker (2cpu/8gb) - two times (k8s/docker vs k8s/docker)

  1. Rerunning the analysis on different executor with same cpu/memory settings

conda vs k8s/docker

  1. Rerunning the analysis on different executor, with scaling of cpu/memory settings

conda (2cpu/8gb) vs conda (8cpu/20gb)

k8s/docker (2cpu/8gb) vs k8s/docker (8cpu/20gb)

Publish on bioarxiv!

abhi18av commented 2 years ago

We can also publish about this pipeline as Application Notes.

abhi18av commented 2 years ago

This benchmarking is done now.