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Running Nextflow pipelines on Puhti

Nextflow is a scalable and reproducible scientific workflow management system that interacts with containerised applications to perform compute-intensive tasks. Nextflow provides built-in support for containers like Singularity, which is a containerisation technology that is compliant with HPC environment. Although Nextflow pipelines allow us to choose Docker engine as an executor for running pipelines, please note that Docker containers can't be used in Puhti due to the lack of administrative privileges for researchers.

Strengths of Nextflow

  • Easy installation
  • No database needed
  • Implicit parallelism supported
  • Can handle complex dependencies and conditional execution
  • Supports error recovery

Disadvantages of Nextflow

  • Limited MPI support
  • May create a lot of job steps and excess IO
  • Does not integrate well with Slurm

How Singularity works with Nextflow

The integration of Singularity containers with Nextflow follows the same execution model as with Docker containers. So it does not require additional modifications in a Nextflow script as such to be compatible with Singularity. One has to just enable the use of Singularity engine (instead of Docker) in the Nextflow configuration file. Nextflow is able to pull remote container images stored in Singularity or Docker-Hub registry. The remote container images are usually specified in your Nextflow script or configuration file by simply prefixing the image name with the shub:// or docker://. It is also possible to specify a different Singularity image for each process definition in the Nextflow pipeline script.

Here is a generic recipe for running your Nextflow pipeline on Puhti :

  1. Prepare your singularity images on your local environment
  2. Login to Puhti supercomputer
  3. Activate the conda environment for Nextflow on Puhti
  4. Set-up your Nextflow pipeline environment
  5. Run your Nextflow pipeline as a batch job
  6. (Optional) tutorial - Demonstration of WtP Nextflow pipeline on Puhti

1. Prepare your Singularity images on your local environment

Singularity containers can't be built directly on Puhti. So one has to build and copy singularity container(s) of a nextflow pipeline from your local environment to Puhti supercomputer.

Here are some options for preparing your singularity image:

  • Build a Singularity image on your local system and then copy it to Puhti
  • Convert a Docker image to Singularity on your local system and then copy it to Puhti.
  • Copy a Singularity image from a container registry to Puhti.

You can also use cPouta environment at CSC to build singularity images.


Singularity is installed only on the compute nodes in Puhti and it is not available for execution or testing on login nodes.

2. Login to Puhti supercomputer

SSH into the login node of Puhti cluster (See instructions here)

Where yourcscusername is the username you get from CSC.

3. Activate the conda environment for Nextflow on Puhti

Nextflow on Puhti is available via a conda environment and is activated as below:

module load bioconda
source activate nextflow

In case you need any custom installations with specific version of Nextflow in your workspace, please follow instructions here.

For the installation of Nextflow, you can use the following conda approach:

export PROJAPPL=/projappl/project_xxx     # Edit the project name
module load bioconda
conda create -n next_flow -c bioconda nextflow=0.30.1  # See note below
source activate next_flow  
Above, next_flow is the name for your env and you can choose which version(s) of nextflow to install

4. Set-up your Nextflow pipeline environment

Running Nextflow pipelines can sometimes be quite compute-intensive and may require downloading large volumes of data such as databases and singularity images. This can take a while and may not even work successfully in case of downloading singularity images on Puhti.

You can do the following basic preparation before running your Nextflow pipeline:

  • Copy singularity images from your local workspace to your project folder on Puhti. Pay attention to the singularity cache directory (i.e., SINGULARITY_CACHEDIR or some other name given by your software tool) which is usually $HOME/.singularity/cache. The disk space of your home directory is quite limited (10 GB) on Puhti.
  • Move all your raw data to your project directory (/scratch/<project name>) on Puhti
  • Clone the GitHub repository of your pipeline to your scratch directory and then run your pipeline. Alternatively, use the Nextflow pipeline directly from DockerHub if the pipeline is available

5. Run your Nextflow pipeline as a batch job

Please follow our instructions for writing a batch job on Puhti as described in CSC documentation pages.

Here is a minimal script to get started with your Nextflow pipeline on Puhti:

#SBATCH --time=00:15:00 # change your time settings
#SBATCH --partition=test #  change partition as needed
#SBATCH --account=project_XXX # add your project number here
#SBATCH --cpus-per-task=xx # change as you need
#SBATCH --mem-per-cpu=1G   # increase as needed

module load bioconda
source activate nextflow

# Actual Nextflow command here
nextflow run  <> [options]

6. (Optional) tutorial - Demonstration of WtP Nextflow pipeline

WtP is a scalable and easy-to-use workflow for phage identification and analysis. More details about the pipeline can be found here.

Login to Puhti and install Nextflow using the conda environment as instructed above.

Set-up WtP pipeline on Puhti

You can either clone the WtP GitHub repository to your project scratch directory as below (remember to edit the project name):

cd  /scratch/project_xxx
git clone
nextflow run /scratch/project_xxx/What_the_Phage/ --help

or pull the Nextflow pipeline from DockerHub:

nextflow run replikation/What_the_Phage  -r v0.8.0 --help

In either case, pay attention to the versions of different singularity containers as mentioned in containers.config file.

Bring your WtP singularity images to Puhti

WtP is a multi-container pipeline requiring as many as 21 singularity images (see here for further details) at the time of writing this tutorial. All these containers were downloaded in cPouta environment to avoid any build failures of singularity images on Puhti due to the lack of privileged access for users. For the sake of this tutorial, the downloaded singularity images were then uploaded to Allas which is an object storage environment at CSC.

The images on Allas object storage can be downloaded to your project directory on scratch as below:

mkdir -p /scratch/project_xxx/What_the_Phage/singularity
cd /scratch/project_xxx/What_the_Phage/singularity
tar -xavf WtP_singularity.tar.gz

Run WtP pipelines as a batch job on Puhti:

Submit the following batch script to run nextflow pipeline:

#SBATCH --time=01:00:00
#SBATCH --partition=small
#SBATCH --account=project_XXX
#SBATCH --cpus-per-task=4

export TMPDIR=$PWD

# Activate  Nextflow on Puhti
module load bioconda
source activate nextflow

# Nextflow command here
nextflow run /scratch/project_xxx/What_the_Phage/ --fasta /scratch/project_xxx/What_the_Phage/test-data/OX2_draft.fa --cores 4 --output results -profile local,singularity --cachedir /scratch/project_xxx/What_the_Phage/singularity --databases /scratch/project_xxx/What_the_Phage/databases/WtP_databases --workdir /scratch/project_xxx/What_the_Phage/workflow-phages-username 

Please note that the Singularity images in this example should be in the folder: "/scratch/project_xxx/What_the_Phage/singularity". Otherwise, Nextflow tries to download the images again which increases the likelihood of failures. Remember to edit project_xxx to match your computing project.

Last update: June 6, 2022