7. SAGA Users

ALPPACA is located here on SAGA:

/cluster/projects/nn9305k/vi_src/ALPPACA

On SAGA we can use our own configuration file, so that the pipeline executes through SLURM. This is located here:

/cluster/projects/nn9305k/nextflow/configs/saga_new.config

To use it, add the -c /cluster/projects/nn9305k/nextflow/configs/saga_new.config parameter to the nextflow run command.

Thus, the full run command would be:

module load Java/17.0.4
nextflow_23.04.1 run /cluster/projects/nn9305k/vi_src/ALPPACA/main.nf -c /cluster/projects/nn9305k/nextflow/configs/saga_new.config <run_parameters>

Profiles

I recommend to run the pipeline using the apptainer profile. Specify -profile apptainer in the run command to activate this.

To make sure that the images used by apptainer/singularity are stored in the correct place, you can add the following lines to the end of your .bashrc file (located in your home directory):

export NXF_SINGULARITY_CACHEDIR=${USERWORK}/images
export SINGULARITY_CACHEDIR=${USERWORK}/images
export NXF_APPTAINER_CACHEDIR=${USERWORK}/images
export APPTAINER_CACHEDIR=${USERWORK}/images

Due to updates with how Nextflow mounts home directories with Apptainer,Singularity,Docker etc, all users need to add the following line to their .bashrc file, depending on which profile you are running with:

export NXF_APPTAINER_HOME_MOUNT=true

If you run with another image handler, replace APPTAINER with f.ex. DOCKER.