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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Add support for running summary modules on command line #60

Closed ewels closed 9 years ago

ewels commented 9 years ago

Currently, you can run a single module instead of a pipeline from the command line. However, it is always run as a regular module, so this is not compatible with summary modules. This is especially problematic when modules can be both normal and summary modules.

Simple to add - allow module names to be prefixed with either # or > when used on the command line (may need quotes). A dynamic pipeline is written from this, so everything should then work downstream.