UsefulOptions - Oshlack/JAFFA GitHub Wiki
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