Closed pinin4fjords closed 6 months ago
We ended up implementing this using fastq_align_star (subworkflow) from nf-core/modules. What nf-core/rnaseq does is a bit messy and complicated by igenomes usage which is not currently very helpful for RNA-studies.
I ended up doing a bit of work alongside to fix up that module for better transcriptome alignment handling: https://github.com/nf-core/modules/pull/4927.
Description of feature
We need both transcriptome and genome alignment for use by different modules associated with Riboseq. This can be adapted from what nf-core/riboseq does.