ccs file as possible input
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rmenafra commented
It would be a nice feature to give the ccs file as an input, therefore skipping the first step (subreads to ccs).
Redmar-van-den-Berg commented
Running CCS and Lima (demultiplexing) have been removed from the pipeline. Version 3.0.0 of the pipeline accepts one or more (per sample) bam files per sample as input.