Add version numbers in VCF output

[mfoll]

It would be good to write at least the pipeline version, nextflow version and the docker container version.

[mfoll]

The .nextflow.logfile contains useful informations:

• nextflow version
• pipeline version
• the command line used to launch it (so if a specific docker image is used it's written too)
• I can't find the docker Image ID

Currently only nextflow version number is accessible with $NXF_VER (see here).

Could we have more environment variables with these informations @pditommaso (pipeline version, docker image ID, eventually the full command line)?

[mfoll]

It could also be useful to obtain the versions of each tool used (in case people don't use docker, and even with docker for easier reference). We could add a process dedicated to that doing:

perl --version
samtools --version
bedtools --version
Rscript --version

And writing all these somewhere in the VCF.
Unfortunately vcflib has no option to display its version number at the moment (requested here).

[pditommaso]

It is not clear how do you want these environment variables. Let's continue the discussion in the nextflow mailing list / gitter / github repo.

[mfoll]

Linked to #41: the log file could be a better place for all details, maybe simply put the pipeline version number in the VCF.

[mfoll]

See nextflow-io/nextflow#79

[mfoll]

Note that it is now also available for vcflib: vcflib/vcflib#102

vcfoverlay -v