A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I'm a big fan of just providing the BAMs from the <#CE8SSJV3N> workflow - less maintenance required to keep parity between the two workflows :+1:

ok as long as there is a way to alternately run salmon and get a count matrix for SUPPA

I agree with both - would be great option in the future to be able to supply BAMs from <#CE8SSJV3N> but would also need to allow users to run salmon on its own and direct that output into SUPPA.

Yep, will be much easier to sponge the pseudo-alignment Salmon subworkflows from <#CE8SSJV3N> and include them here rather than all of the steps that go into the BAM generation.