Make a script that would run needlestack without nextflow

[mfoll]

It should be easy to simply take the shell portions from nextflow script. Of course we just ignore the first one splitting the bed file. The difficult part could be to parse arguments (and to give them the same names) and to make sure we keep it up-to-date when we update the nextflow script. For arguments parsing, have a look at https://gist.github.com/jehiah/855086

[mfoll]

Should be easy after #147