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UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
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Parallelize `sort` process #38

Closed fanninpm closed 3 years ago

fanninpm commented 3 years ago

Previously, I had to reduce the number of reserved CPUs for this step, as the command did not use every allocated core. A cursory look on GitHub revealed the -@ option, which is documented as "threads" in the samtools manual.

erinyoung commented 3 years ago

I didn't notice that there was this option for samtools sort! I wonder how long it's been there and I just didn't notice.

Thank you for the pull request!

fanninpm commented 3 years ago

Should I make a similar PR in the StaPH-B repo?

erinyoung commented 3 years ago

I wouldn't worry about that. The two cecret workflow files are connected.

fanninpm commented 3 years ago

I wouldn't worry about that. The two cecret workflow files are connected.

I wouldn't be so sure...

https://github.com/StaPH-B/staphb_toolkit/blob/7523cec6ea78a8deb23fe94b3fed34d3bdef7aee/staphb_toolkit/workflows/cecret/cecret.nf#L419

erinyoung commented 3 years ago

It should be in the pull request over there now. It took awhile to get this release out.