Providing fragment estimated for SE kallisto

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

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Providing fragment estimated for SE kallisto #107

Closed darogan closed 7 years ago

darogan commented 7 years ago

Single end kallisto requires an estimate of the fragment length, either from bioanalyser or a best guess based on typical library preps

ewels commented 7 years ago

Great, thanks!

ewels commented 7 years ago

Hi @darogan,

I just tweaked your change a little in 1e357255b2a05b09d01aae336684cc2cdd898d03 - I made the two new variables configurable by setting Cluster Flow parameters, so that people can easily change them if they want to. They still default to 200 and 20 so it should work in the same way.

Phil

darogan commented 7 years ago

I was going to suggest the variables should be user definable, but the defaults should be OK for most cases.

I'm just tidying up my cf install and getting back into sync with your main branch. I have some more modules to add at some point