STAR 2-pass alignment

[siebrenf]

          I remembered that I read somewhere, you do not support 2-pass start alignemnt yet.  What is your recommendation if we want to do the two passes, and then come back to Seq2science again?

Originally posted by @bioinfolabmu in #1018 (comment)

[siebrenf]

1. prepare the RNA-seq workflow as usual
2. run the RNA-seq workflow until the STAR alignment is completed. Example command: seq2science run rna-seq --snakemakeOption until=[samtools_presort] (you could continue until after mark_duplicates too)
3. manually run the STAR output through the 2nd pass

Optional:
4. overwrite the output from the 1st pass with the output from the 2nd pass
5. restart the seq2science workflow (without the until argument) to continue with the QC and count matrix steps.

Please note: STAR's 2nd pass outputs splice site information IIRC. I don't know if the seq2science processing can make use of this, so steps 4 and 5 may not do anything, or even work!