This PR adds a starsolo workflow to the genetic demultiplexing folder as part of #127
While the end result is fairly simple, finding the exact sets of parameters so things would run consistently & without error was a bit of a challenge! In particular, the BAM sorting is finicky, but required for some of the SAM output fields that I think we will need for cellsnp later.
I separated the BAM output and starsolo quantification into different outputs, as I don't expect to need both downstream. I had considered skipping the quantification completely, but we do need it for some of the SAM output fields (maybe I can find the combination that doesn't require all of that, but the quantification is not the slow part, so I left it).
There is some redundancy here with the bulk workflow (bam indexing) but I left it for now, as I expect to do separate set of PRs where I integrate everything after individual steps work.
This PR adds a starsolo workflow to the genetic demultiplexing folder as part of #127
While the end result is fairly simple, finding the exact sets of parameters so things would run consistently & without error was a bit of a challenge! In particular, the BAM sorting is finicky, but required for some of the SAM output fields that I think we will need for cellsnp later.
I separated the BAM output and starsolo quantification into different outputs, as I don't expect to need both downstream. I had considered skipping the quantification completely, but we do need it for some of the SAM output fields (maybe I can find the combination that doesn't require all of that, but the quantification is not the slow part, so I left it).
There is some redundancy here with the bulk workflow (bam indexing) but I left it for now, as I expect to do separate set of PRs where I integrate everything after individual steps work.