recipe jaffa

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts then searches for gene fusions. This package contains the wrappers jaffa-direct, jaffa-assembly, and jaffa-hybrid. You can pass the "refSeq" parameter in the environment variables JAFFA_REF_BASE. Otherwise, pass any paramters to the wrappers as you would to the bpipe JAFFA_{method} call in the manual.






package jaffa

(downloads) docker_jaffa



depends bbmap:

depends bioconductor-iranges:

depends blat:

depends bowtie2:

depends bpipe:

depends fastx_toolkit:

depends oases:

depends samtools:


depends trimmomatic:

depends velvet:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install jaffa

and update with::

   mamba update jaffa

To create a new environment, run:

mamba create --name myenvname jaffa

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `jaffa/tags`_ for valid values for ``<tag>``)

Download stats