Latebreaking additions to workflow to reduce dependancy on dowloading BAMs

NOTE: readme details minor installation changes, particularly which items still need apt-get when pulling pre-compiled code from Artifactory.

Changes to workflow to include:

Gneration of count/gc/allele bin files similar to thouse used in legacy PICNIC NGS tools, these have been found to be usedful for downstram analysis of rearrangments.
Primary benefit is that with these available we should be able to use minor slicing while developing more accuraterearrangment analysis.

Base allele counts files based on impute 1000 genomes loci, this is the only input required for Battenberg and they may be of use to others, sadly not VCF but time constrainsts prevented adding conversion.
Replicate new memory parameters to bionimbus ini
Removed unnecessary step.
File type was made to match format
Missing include path
Invalid pathing
Should now use the new testdata.
Minor pathing issue, update bionimus version of ini too.
Give cram to bam conversion 2 threads.
Fix path error
BAM index has to be regenerated following bam->cram->bam
No point copying the rest as they aren't needed or need regenerating.
testMode (use packaged test data) now physically blocks uploads.
Spoke to soon, should be the final pathing issue
Handle an error in the test file header so that we can get this running
Multi-command syntax issues
Small error in perl one-liner
Missing redirect
Wierdness with line feeds in commands, switched to ';'
Missing critical line