[minor] Better handling of skipping ERCC process

czbiohub-sf / sc2-illumina-pipeline

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

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[minor] Better handling of skipping ERCC process #71

Open jackkamm opened 3 years ago

jackkamm commented 3 years ago

The quantifyERCCs step should only happen when doing MSSPE sequencing, not ARTIC sequencing.

Currently, we de facto skip it for ARTIC -- in particular, we still run the process, but just create a dummy output. However it would be better to skip the process entirely.

A slight complication is that one of the downstream processes (computeStats) consumes the output of quantifyERCCs, which is why we created the dummy output instead of skipping the process entirely.

jackkamm commented 3 years ago

Closing as stale/minor/unimportant

danrlu commented 3 years ago

Can implement while migrating to DSL2. Will leave as is if complicated.