Versions

Hi, Phil, I wanted to include the version numbers of the programs called by clusterflow in the run report file for --verbose mode, so I edited the cfmod files for samtools, bowtie etc. to output this to the clusterflow report file if "report_v" is in the params (--verbose now adds "report_v" to the params fed to all modules). For some programs it's impossible to get version info without also getting the help page, I could have pared this down (e.g. htseq-count | tail -n 3 ) but I chose not to because we can't predict the format of future versions of their help pages.

Anyway I also noticed that the report file for some reason doesn't recognise some of its own output, from the email scheduling cfmod it looks like. It's not a serious issue. I tagged unrecognised output with arrows in the report file to highlight it too.