Define `threads` in config file

snystrom / cutNrun-pipeline

Analysis pipeline for CUT&RUN Data. Currently configured for use in the McKay Lab at UNC, but extensible elsewhere by changing configuration files.

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Define `threads` in config file #23

Open snystrom opened 4 years ago

snystrom commented 4 years ago

Because you can't pull from cluster config file inside Snakefile, have a flag in the config.json which includes number of cores to use for alignment. Query this variable in the threads: definition of the alignment rule.

Idea: Scale threads based on ref vs spike genome?