Separated from a private correspondence: the RNA-seq DE example workflow now is broken. To reproduce:

cd sos-docs/src/examples
sos run RNASeqDE.ipynb align -j 2 --samples SRR1039508

Error message:

ERROR: Multiple steps hg19_reference_1, hg19_reference_2, hg19_reference_3 to generate target sos_step("hg19_reference")

This used to work, though. I guess maybe it is similar to issue in #981 introduced due to recent changes of target dependency codes.