Tagged with #rsem
0 documentation articles | 0 announcements | 1 forum discussion

No articles to display.

No articles to display.

Created 2014-03-03 09:19:41 | Updated 2014-03-03 09:20:25 | Tags: queue commandline rsem

Comments (3)

I'm working on add RSEM to our RNAseq pipeline which uses Queue. RSEM takes a number of inputs on the command line, so I have a case class and override commandLine for this to work. Nothing special there.

However, RSEM wants a prefix of the output sample names. If i give it sample_name, it will generate a whole bunch of files, sample_name.genes.results with expression values for genes, sample_name.isoforms.results with expression values for isoforms, sample_name.genome.bam, sample_name.genome.sorted.bam and sample_name.genome.sorted.bam.bai with mappings etc, etc.

What's the best way to handle this in terms of @Output?

Should I use (1):

case class rsem(inFq1: File, inFq2: File, prefix: String) extends ExternalCommonArgs {
   @Output val myPrefix = prefix

and them use the prefix in the downstream jobs? Or should I use (2):

case class rsem(inFq1: File, inFq2: File, prefix: String, bam: File, geneResults: File) extends ExternalCommonArgs {
   @Output val myBam = bam
   @Output val myGeneRes = geneResults

In (2), I would still use prefix in the def commandLine, of course.

Is there a preferred way to handle this in Queue?