davidsongroup/jaffa repository overview

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions. It will output the names and locations of candidate gene fusions along with the cDNA sequence of their breakpoints. JAFFA is based on the idea of comparing a transcriptome (e.g. in a cancer sample) against a reference transcriptome. In this way, it is a transcript-centric approach rather than a genome-centric approach like other fusion finders. In validation studies, JAFFA performed well over a range of read lengths - from 50bp to full-length transcripts and on single and paired-end reads.

More information about JAFFA can be found at the wiki⁠ and the GitHub⁠.

This is the official container image for JAFFA. The container image bundles all dependencies, so all you will need is a container platform such as Docker or Apptainer (formerly Singularity). As an added bonus, everything is prebuilt, so all you need to do is wait for a ~700MB compressed image download. This image has the same functionality as the regular version of JAFFA.

The JAFFA image does not bundle reference files. You will need to download the reference files and extract them into any directory, let's say $REF_DIR. JAFFA expects references to be found under /ref/, so you will need to bind this. All pipeline files (JAFFA_direct.groovy, JAFFA_assembly.groovy, JAFFA_hybrid.groovy, JAFFAL.groovy) can be found under the /JAFFA/ directory.

An example of running JAFFA in a container, comparing Docker/Apptainer with a native run:

REF_DIR=/path/to/references
INPUT_DIR=/path/to/input

# native command, after installing and configuring the reference directory
JAFFA_PATH=/path/to/jaffa
$JAFFA_PATH/tools/bin/bpipe run $JAFFA_PATH/JAFFA_direct.groovy $INPUT_DIR/*.fasta <parameters>

# Docker command
docker run                                \
    -B $REF_DIR:/ref                      \
    -B $INPUT_DIR                         \
    davidsongroup/jaffa:latest            \
    /JAFFA/JAFFA_direct.groovy            \
    $INPUT_DIR/*.fasta                    \
    <parameters>

# Apptainer/singularity command
apptainer run                             \
    -B $REF_DIR:/ref                      \
    -B $INPUT_DIR                         \
    docker://davidsongroup/jaffa:latest   \
    /JAFFA/JAFFA_direct.groovy            \
    $INPUT_DIR/*.fasta                    \
    <parameters>