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nf-core / riboseq

Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
https://nf-co.re/riboseq
MIT License
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Add alignment #14

Closed pinin4fjords closed 6 months ago

pinin4fjords commented 6 months ago

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.

pinin4fjords commented 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.