Add option to ignore -e flag in stringTie

[husensofteng]

The -e flag in stringTie forces it to only report transcript that are found in the reference GTF file. Skipping the -e flag below would enable performing reference-guided de novo assembly.

rnaseq/main.nf

Line 1032 in 37f260d

-e \\

I wonder if it would be possible to add a parameter to skip this flag.

[drpatelh]

--stringTieIgnoreGTF parameter has been added in PR #195, and will be fixed when the salmon branch is merged into dev