Useful command line options

Here are the command line options that I've found most useful when running JAFFA.

Bpipe commands:

• run - run the pipeline!
• test - print the next stage in the pipeline which will be run (without actually running it)
• history - tells you previous bpipe commands you've run. This makes it easy to rerun the same command again
• log - a log of all the info bpipe outputs to stdout. This can be useful for monitoring jobs which are running in the background.

Bpipe options:

• -n - set the number of threads
• -r - will create a html report of the running time for the pipeline.
• -p - set a JAFFA option (see below)

JAFFA options:

• readLayout - used to specify single end reads (otherwise paired is assumed). e.g. -p readLayout="single"

• genome and annotation- should be used to change the reference from the default of hg19. e.g. -p genome=mm10 -p annotation=genCodeVM4

• refBase - sets the location of the reference files for JAFFA if outside the code installation area. e.g. -p refBase=<ref directory>

• exclude - set which types of fusions are filtered out. e.g. -p exclude="NoSupport" will allow read-through transcription to be reported (filtered by default).

• see the variables at the head of JAFFA_stages.groovy for a full list