rename output options

[mfoll]

Currently the --output_vcf parameter can only be the name of the file and not the full path (see https://github.com/IARCbioinfo/needlestack/blob/v1.1b/needlestack.nf#L505 and https://groups.google.com/forum/#!topic/nextflow/ctLboXGPdwI), and the path can be given using --output_folder.

The rational was that the output also includes a PDF folder. However this can be confusing as putting the path in output_vcf is tempting. I propose to change the behaviour as follow:

--output_vcf: is the path to the output vcf (e.g. my_vcf.vcf or /path/to/my_vcf.vf or ../my_vcf.vcf) --output_pdf: is optional and is the folder where to store the PDF folder (e.g. . or /path/to/outfolder). If absent, we put it in the same folder as the --output_vcf folder (to be extracted from the it). --output_folder no longer exists.

Any objection or better idea?