How to launch MouseFlow

Local computer

To run the pipeline, use the following command:

# With Singularity
$> nextflow run scilus/nf-mouse_flow -r 0.1.0dev --input input_folder -profile singularity --atlas atlas_directory -resume

If you want to skip steps already processed by an anterior run, you can add -resume option in the command line.

High Performance Computer (HPC)

The following example is based on the SLURM executor:

Before running the pipeline you will need to download the singularity images needed to run your pipeline. You can do this by running the following command:

$> nextflow pull scilus/nf-mouse_flow -r 0.1.0dev

If you want to run mouseflow, please use the same commands presented for the local computer. The following lines must be saved in .sh file (e.g. cmd.sh) to be executed with sbatch.

#!/bin/sh

#SBATCH --nodes=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=0
#SBATCH --time=48:00:00

nextflow run scilus/nf-mouse_flow -r 0.1.0dev --input input_folder -profile singularity --atlas atlas_directory -resume