User installation

FlowCraft is available as a bioconda package, which already comes with nextflow:

conda install flowcraft

Alternatively, you can install only FlowCraft, via pip:

pip install flowcraft

You will also need a container engine (see Container engine below)

Container engine

All components of FlowCraft are executed in docker containers, which means that you’ll need to have a container engine installed. The container engines available are the ones supported by Nextflow:

If you already have any one of these installed, you are good to go. If not, you’ll need to install one. We recommend singularity because it does not require the processes to run on a separate root daemon.


Singularity is available to download and install here. Make sure that you have singularity v2.5.x or higher. Note that singularity should be installed as root and available on the machine(s) that will be running the nextflow processes.


Singularity is available as a bioconda package. However, conda installs singularity in user space without root privileges, which may prevent singularity images from being correctly downloaded. Therefore it is not recommended that you install singularity via bioconda.


Docker can be installed following the instructions on the website: To run docker as anon-root user, you’ll need to following the instructions on the website:

Developer installation

If you are looking to contribute to FlowCraft or simply interested in tweaking it, clone the github repository and its submodule and then run

git clone
cd flowcraft
git submodule update --init --recursive
python3 install