-h open help page

-d perform a dry-run of the pipeline

-f specify your config-file (required)
copy the example config-file to a desired location and change the parameters within
attention!: do not alter the example.config.yaml file! in case of an update of the pipeline, it will be overwritten!

-c run on a slurm cluster cluster file can be provided. Default: assumes a cluster.json in your working directory

-p make a plot of the DAG structure

-j specify how many jobs should be submitted in parallel (only on cluster). Default: 50

\\ citations for used scripts and programms in this pipeline: \\ \\ \\ \\ This script is available free of use at \\ \\ https://bitbucket.org/wegmannlab/adnapipeline.bam/src/master/ \\ \\ for questions correspond to ilektra.schulz@unifr.ch \\ \\ To pull the newest version, run \\ \\ git clone https://iSchulz@bitbucket.org/wegmannlab/adnapipeline.bam.git \\ \\ \\ \\ within the script, the following programs, in addition \\ \\ to the programs listed in environment_recent.yaml were used: \\ \\ GATK: https://software.broadinstitute.org/gatk/ \\ \\ \\ \\ Snakemake: http://snakemake.readthedocs.io/en/stable/index.html \\ \\ \\ \\ No guarantee for the content and results of this script to be bug-free. \\