#! /bin/bash
#SBATCH -D .
#SBATCH -o log.%x.%j
#SBATCH -J nf_flux_hwt
#SBATCH --get-user-env
#SBATCH -M cm4
#SBATCH -p cm4_tiny
#SBATCH --qos=cm4_tiny
#SBATCH --nodes=1-1
#SBATCH --ntasks-per-node=2
#SBATCH -c 112
#SBATCH --hint=multithread
#SBATCH --export=none
#SBATCH --time=1-00:00:00

module load slurm_setup

module load micromamba
micromamba activate $SCRATCH_DSS/env_nfcore

cat > workflow.sh << EOT
nextflow run nf-core/rnaseq -c lrz_cm4.config --input samplesheet.csv
flux jobs -a
EOT
chmod u+x workflow.sh

srun --export=all --mpi=none flux start ./workflow.sh