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ewels / clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
https://ewels.github.io/clusterflow/
GNU General Public License v3.0
97 stars 27 forks source link

Geopts #12

Closed stu2 closed 9 years ago

stu2 commented 9 years ago

Hi Phil, there's 2 main things in this PR, first a proper pre-runtime runfile parser for the memory / cores estimation in .cfmods, and a more sensible array of information passed to these from cf so they can make their decision on the memory request. An example of parsing them is in the example cfmod. Second, I added hardcoded genome paths for the STAR aligner and a .cfmod wrapper for that. I gather you're looking to get rid of hardcoded paths soon, but it works as a temporary measure. I've only tested these on our cluster which can't use the shared memory options that STAR is capable of. Also fixed some bugs and added more control of trim_galore from the pipeline args. I might add a sambamba wrapper later, but I think that's it from me for the time being, it's got everything I wanted :) Cheers, Stuart

ewels commented 9 years ago

Hi Stuart,

Apologies for the delay - I was away last week. Code looks really nice, thanks! I've added a few comments as I went through the code, they're all very minor though. Feel free to act on them or ignore, just let me know and I'll merge.

Cheers,

Phil

ewels commented 9 years ago

Ok, I'll merge the other PR instead.