Fixes for --skip_demultiplexing in setup

cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.

https://iguide.readthedocs.io/en/latest/

GNU General Public License v3.0

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Fixes for --skip_demultiplexing in setup #41

Closed ressy closed 5 years ago

ressy commented 5 years ago

This updates the setup script to make --skip-demultiplexing allow an existing demultiDir and pass the config info along to get_sample_list. Fixes #40.

ressy commented 5 years ago

Actually it looks like there'd probably be more needed to make this functional. During a run the generate_state_matrix rule wants the .stat files that come from the demultiplex rule, I just noticed. Maybe concatenating everything and letting iGUIDE do the usual demultiplexing is best after all?

cnobles commented 5 years ago

Closed in favor of #51, which includes additional functionality.