I am trying to code a simple rna seq workflow that will use dataset collections. I want to support multiple paired-end samples, with multiple replicates.
I have scoured the web, but can't seem to find instructions or examples.
I found this video instructing me how to create a multi-replicate paired-end dataset collection, which is helpful: https://vimeo.com/163625221
But I haven't found any examples of writing workflows that consume such a dataset collection. The closest I found, which isn't all that helpful, was Figure 15 here: https://galaxyproject.org/tutorials/collections/
My flow is: trimmomatic -> hisat2 -> htseq-count -> DESeq2
I don't understand how to wire it, such that all the replicates work.
There are probably examples someplace, but I don't know where to look.