Add option for turning on/off STAR command line option (--sjdbGTFfile)

[ladyjkalx]

To save on compute time and cost (AWS), I am running the nf-core/rnaseq pipeline on pre-built STAR genome index files. When using pre-built indexes, re-mapping gtf annotations on the fly from the .gtf file is not necessary. The STAR pipeline has an option for turning this gtf mapping on or off: "--sjdbGTFfile "/path/to/ann.gtf". Currently the gtf option is hard-coded "on" in the nf-core/rnaseq pipeline. It would be helpful if this option could be turned on/off in user-defined configuration files.

[drpatelh]

I have added a new parameter --star_ignore_sjdbgtf to enable this behaviour @ladyjkalx. This will be in the next release which will be in DSL2 and hopefully more customisable overall for adding / removing optional parameters.