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.

Homepage

https://github.com/Oshlack/JAFFA

License

GPLv3

Recipe

/jaffa/meta.yaml

package jaffa

(downloads) docker_jaffa

Versions

1.09-1, 1.09-0, 1.08-0

Depends bbmap

Depends bioconductor-iranges

Depends blat

Depends bowtie2

Depends bpipe

Depends fastx_toolkit

Depends oases

Depends samtools

1.1

Depends trimmomatic

Depends velvet

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install jaffa

and update with:

conda update jaffa

or use the docker container:

docker pull quay.io/biocontainers/jaffa:<tag>

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