search

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

Picard dedup module does not use the TMPDIR #109

Closed jherrero closed 8 years ago

jherrero commented 8 years ago

In typical cluster configurations where the working directory is a shared (i.e. lustre) folder, it is best to tell Picard to use the local temporary directory for the deduplication.

In our setup, this translates in a 4x speed increase.