How to launch TractoFlow
Local computer
To run the pipeline, use the following command:
# With Singularity
$> nextflow run tractoflow -r 2.4.3 --bids input_bids -with-singularity scilus_1.6.0.sif -resume
# Or
$> nextflow run tractoflow -r 2.4.3 --input input_folder -with-singularity scilus_1.6.0.sif -resume
# With Docker
$> nextflow run tractoflow -r 2.4.3 --bids input_bids -with-docker scilus/scilus:1.6.0 -resume
# Or
$> nextflow run tractoflow -r 2.4.3 --input input_folder -with-docker scilus/scilus:1.6.0 -resume
# If you have an NVIDIA GPU installed
$> nextflow run tractoflow -r 2.4.3 --bids input_bids -with-singularity scilus_1.6.0.sif -profile use_gpu -resume
# Or
$> nextflow run tractoflow -r 2.4.3 --input input_folder -with-singularity scilus_1.6.0.sif -profile use_gpu -resume
If you want to skip steps already processed by an anterior run, you can add -resume option in the command line.
High Performance Computer (HPC)
The following example is based on the SLURM executor:
If you want to run tractoflow, please use the same commands presented for the
local computer. The following lines must be saved in .sh
file (e.g. cmd.sh
)
to be executed with sbatch
.
#!/bin/sh
#SBATCH --nodes=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=0
#SBATCH --time=48:00:00
nextflow run tractoflow -r 2.4.3 --input input_folder -with-singularity singularity_name.sif -resume
To launch tractoflow on a node with a GPU, you must use the profile use_gpu in your command.
The following example use one node with gpu. The following lines
must be saved in .sh
file (e.g. cmd.sh
) to be executed with sbatch
.
#!/bin/sh
#SBATCH --nodes=1
#SBATCH --gpus-per-node=v100:1
#SBATCH --cpus-per-task=32
#SBATCH --mem=0
#SBATCH --time=48:00:00
export NXF_CLUSTER_SEED=$(shuf -i 0-16777216 -n 1)
nextflow run tractoflow -r 2.4.3 --input input_folder -with-singularity singularity_name.sif -resume -profile use_gpu
To launch the pipeline on the HPC:
$> sbatch cmd.sh