--work-dir not used?

[prmac]

Setting --work-dir does not appear to change the default location of work.

[apeltzer]

--outdir is for output files, -w / -work-dir for working directory, but this comes from Nextflow itself.

[prmac]

Doc states
-w/--work-dir The temporary directory where intermediate data will be saved
So if I change this I would anticipate the Nextflow "work" directory being output to the location I provide? However that folder and all intermediate files are output to the directory the cextflow command is run from.

[prmac]

https://github.com/nf-core/rnaseq/blob/master/main.nf#L93
Line shpuld read -work-dir not --work-dir

[apeltzer]

True, this is a typo in the help then - feel free to open a PR to adress this, otherwise someone else will take care :-)

[apeltzer]

Fix is in #442