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