This repository provides a starting point to using three popular scientific workflow managers - Nextflow, Cromwell, and Snakemake. This material is used as instructional material for the Research IT workshop.
In order to use these workflow managers, first download Miniconda3. This can be done on the command line (assuming you are using our Linux cluster) by doing the following. First, navigate to a directory in which you have at least a few GB of available space. Then, use the following commands.
wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
Once Miniconda is installed, you can then download the required software. Clone the repository, and then run install.sh to install the pre-made conda environment.
git clone https://github.com/TheJacksonLaboratory/wfm.git
cd wfm
bash install.sh
This will create a conda environment named wfm, as well as download the Nextflow and Cromwell execution engines into their designated folders. Now you're ready to start using these examples!
For reference, here are the commands that are used to run each of these examples. To run an example, you must first cd into the respective directory. Also, please ensure that you have activated the wfm conda environment by running conda activate wfm.
nextflow pipeline.nf
java -Dconfig.file=[parent-directory]/wfm/cromwell/my.conf -jar cromwell-54.jar run -i inputs.json pipeline.wdl
OR
bash start (Included for convenience)
snakemake -j1 --profile ./slurm