evoverse_job_nf

#!/bin/sh
#### Cluster specific arguments ####

#SBATCH --job-name=NF_MASTER
####SBATCH --output=logs/nf_%j.out
#SBATCH --error=err
#SBATCH --partition=THIN
#SBATCH --nodes=1
#SBATCH --ntasks=2
#SBATCH --cpus-per-task=1
#SBATCH --mem=10G
#SBATCH --time=12:00:00
#SBATCH -A cdslab
#SBATCH --output=log

module load singularity/3.10.4
module load java/1.8.0
module load R/4.2.3

RESULTS_PATH=$evoverse/results/single_sample/

/orfeo/LTS/CDSLab/LT_storage/ncalonaci/nextflow/nextflow run $evoverse/main.nf \
    -c $evoverse/modules/config/nextflow_config_slurm \
    --samples $evoverse/evoverse_input.csv \
    --publish_dir $RESULTS_PATH \
    --mode "singlesample" \
    --tools "pyclone-vi,mobster,viber,sparsesignatures" \
    --pyclonevi_n_cluster 5 \
    --pyclonevi_n_restarts 10 \
    --mobster_samples 1 \
    --mobster_K 2 \
    --viber_K 4 \
    --viber_samples 1 \
    --viber_maxIter 50 \
    --sparsesignatures_cross_validation_repetitions 10