How to launch extractor_flow

Local computer

To run the pipeline, use the following command:

# With Singularity
$> nextflow run extractor_flow -r 1.0.0 --input input_folder -with-singularity scilus_flow_1.5.0.sif -resume

# With Docker
$> nextflow run extractor_flow -r 1.0.0 --input input_folder -with-docker scilus/scilus_flows:1.5.0 -resume

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

CBRAIN

High Performance Computer (HPC)

The following example is based on the SLURM executor:

If you want to use only one node, please use the same commands presented for the local computer. The follwing 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 -c singularity.conf run extractor_flow -r 1.0.0 --input input_folder -with-singularity singularity_name.sif -resume

To launch on multiple nodes, you must to use the MPI option that use Ignite executor. The following example use 2 nodes with 32 threads on each nodes. The follwing lines must be saved in .sh file (e.g. cmd.sh) to be executed with sbatch.

#!/bin/sh

#SBATCH --nodes=2
#SBATCH --cpus-per-task=32
#SBATCH --mem=0
#SBATCH --time=48:00:00

export NXF_CLUSTER_SEED=$(shuf -i 0-16777216 -n 1)

srun nextflow -c singularity.conf run extractor_flow -r 1.0.0 --input input_folder -with-singularity singularity_name.sif -with-mpi -resume

To launch the pipeline on the HPC:

$> sbatch cmd.sh