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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
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Get Bismark summary module to use new bismark command #87

Closed ewels closed 8 years ago

ewels commented 8 years ago

The new v16 release of Bismark included a new bismark2summary command which creates a summary report. Now that this is part of the core bismark package, there's no need to keep this code in a Cluster Flow module. So, we can massively simplify the bismark_summary_report module and just get it to call the new bismark2summary command instead.

ewels commented 8 years ago

Would also be nice to add --nucleotide_coverage to the main bismark command.

FelixKrueger commented 8 years ago

Just as a word of warning, adding --nucleotide_coverage might add a few extra hours of processing time, at least for the first pass of the reference genome.

ewels commented 8 years ago

Yup, thanks for the heads up! I think I'll leave this for now, at least until FelixKrueger/Bismark#44 is cleared up and I've tested the extra time needed.