example rnaseq data yields no gene expression with stringtie

[chrisamiller]

If I pull down the example data and run the rnaseq yaml through the current rnaseq.cwl, kallisto returns per-transcript and per-gene abundance, but stringtie does not - all the FPKM/TPM values are 0

Example command: /usr/bin/java -Dconfig.file=cromwell.config -jar /opt/cromwell.jar run -t cwl -i rnaseq.yaml definitions/pipelines/rnaseq.cwl

I'm unclear what the issue is at this point