CM5 is your pipe of choice, if you want to run more than 30 oligos (more feasible visualisations), or have multilane data (no catenation of input fastq files needed any more).
The default parallelisation unit is 4 processors, and you can change this with flag -p 4 . If the queue looks empty-ish, you can freely give more than 4. Submit the run to the queue normally - it will take care of the parallelisation on its own. If you have a lot of fastqs, and/or hundreds of capture sites, you may want to run in "wholenode mode" , and submit to wholenode queue instead (instructions below).
/t1-data/data/hugheslab/jelenatools/CCseqBasic/CM5/pipeRainbow.sh -h
Output folder structure and rerun options (a draft to become the user manual)
Wholenode style run instructions (a draft of user instructios for this special run style)