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cancerit / cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
http://cancerit.github.io/cgpPindel/
GNU Affero General Public License v3.0
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Naive question, does increasing -c in pindel input will make it faster? #90

Closed jsmedmar closed 4 years ago

jsmedmar commented 4 years ago

The docs suggest to use 4 cores for Pindel Input, I'm just curious why 4? Would, say, 8 make it faster?

Thank you so much for your time in advance

keiranmraine commented 4 years ago

If you are running as pindel.pl ...-p input -i N then setting 4 is the maximum as that is the max for the underlying process (beyond this it will get slower).

If you are running as a "one shot" either just defining -p input (no -i) or no -p at all, then 8 is valid.

Please note that from v3.2.0 onwards the input step is significantly faster anyway, so 2-3 is probably optimum.

I'd honestly recommend trying 1,2,3 and 4 to check the benefit, ultimately you only need to test this script for that bit:

https://github.com/cancerit/cgpPindel/blob/dev/perl/bin/pindel_input_gen.pl

keiranmraine commented 4 years ago

Also note:

https://github.com/cancerit/cgpPindel/blob/93dce3cb25adaa4b34c2e92d70b86f5c11ef9266/perl/bin/pindel_input_gen.pl#L85-L88

jsmedmar commented 4 years ago

This is really useful, thanks so much for clarifying