To run the pipeline you must install Nextflow. To use our Singularity container, you must install the Singularity package.


Note that the below sections use nextflow version v21.10.6 for illustrative purposes: newer versions might work or be required depending on the pipeline at issue.

⚠️ Tractoflow is only compatible with nextflow versions between 19.04.2 and 21.12.1 included. ⚠️

Local Computer

  1. Before installing check your current version java -version. If return something as java version "1.X" and X is 8 up to 11, you can skip this step else install java.

  2. Install Nextflow:

$> wget && chmod +x nextflow && \
echo 'export PATH=$PATH:'$(pwd) >> ~/.bash_profile && source ~/.bash_profile

High Performance computer (HPC)

  1. Try module load nextflow/21.10.6 or check with your administrator or on the HPC website.

  2. Use wget to install Nextflow, change the name, add execution rights and add the Nextflow path in the bash_profile.

$> wget && \
mv nextflow-21.10.6-all nextflow && \
chmod +x nextflow && echo 'export PATH=$PATH:'$(pwd) >> ~/.bash_profile && source ~/.bash_profile

Note that a given HPC system might offer (a) readily available nextflow version(s). If any of provided versions suffice for the pipeline at issue, the above step can be omitted, and reading the documentation of the HPC system is encouraged in order to load the suitable version. In the case of the Alliance Canada clusters, the above step might be substituted by adding the line module load nextflow/21.10.6 (depending on the desired and available versions) to the .bash_profile file and sourcing it.


Our Singularity container currently works on Linux. We highly recommend to use Singularity on a Linux local computer or on a HPC.

If you want to use Docker on Windows or MacOS, please see the Docker for TractoFlow section.

Local Computer

Install apptainer. Our current singularity container works only on Linux.

$> sudo apt-get update && sudo apt-get install -y apptainer

High Performance computer (HPC)

Please try module load apptainer or check with an administrator or on the HPC website.



To install Docker on your MacOS computer, please check the following link:


To install Docker on your Windows computer, please check the following link: