This PR fixes an issue that I noticed where the idNonBovis was not running correctly after being moved to a standalone script. I picked this up running samples which do not 'Pass'. There were a number of problems, but they have all been fixed:
Additional parameters (kraken2db and lowmem) were required when calling the script - without them kraken fails and does not produce the output for bracken.
Bracken also required the kraken2db parameter (and the kraken output!).
In addition to bracken being linked in /usr/local/bin, the bracken/src/ directory also need to be linked.
the awk command failed as the variables were escape (which was essential to get it running as a script embedded in nextflow)
This PR fixes an issue that I noticed where the idNonBovis was not running correctly after being moved to a standalone script. I picked this up running samples which do not 'Pass'. There were a number of problems, but they have all been fixed: