imbforge/rnaseq repository overview

RNA-seq standard pipeline. Run with (as root):

docker run --rm -v ${WORKDIR}:${WORKDIR} -w ${WORKDIR} -t imbforge/rnaseq:v1 -n ${MAX_PARALLEL_PROCS} ${WORKDIR}/rnaseq_v1.2.txt ${WORKDIR}/rawdata/*.fastq.gz

where ${MAX_PARALLEL_PROCS} is the number of tasks to be run in parallel (be careful some tasks already use 4 threads --> defined in the global essential.vars.groovy config file or the module specific config file module.vars.groovy)

To run an interactive shell (the exported filesystems from the host machine can still be mounted with -v):

docker run --rm --entrypoint=/bin/bash -ti imbforge/rnaseq:v1 -s