backend hpc
Either miniwdl or Cromwell can be used to run workflows on the HPC.
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miniwdl>= 1.9.0 miniwdl-slurm
An example miniwdl.cfg file is provided here. This should be placed at ~/.config/miniwdl.cfg and edited to match your slurm configuration. This allows running workflows using a basic SLURM setup.
Cromwell supports a number of different HPC backends; see Cromwell's documentation for more information on configuring each of the backends. Cromwell can be used in a standalone "run" mode, or in "server" mode to allow for multiple users to submit workflows. In the example below, we provide example commands for running Cromwell in "run" mode.
Fill out any information missing in the inputs file. Once you have downloaded the reference data bundle, ensure that you have replaced the <local_path_prefix> in the input template file with the local path to the reference datasets on your HPC.
See the inputs section of the singleton README for more information on the structure of the inputs.json file.
miniwdl run workflows/singleton.wdl --input <inputs_json_file>cromwell run workflows/singleton.wdl --input <inputs_json_file>
Reference data is hosted on Zenodo at 10.5281/zenodo.14027047. Download the reference data bundle and extract it to a location on your HPC, then update the input template file with the path to the reference data.
## download the reference data bundle
wget https://zenodo.org/record/14027047/files/hifi-wdl-resources-v2.0.0.tar
## extract the reference data bundle and rename as dataset
tar -xvf hifi-wdl-resources-v2.0.0.tar