nextflow.slurm

#!/bin/bash

#SBATCH --job-name=rnaseq-nextflow
#SBATCH --partition=batch
#SBATCH --error=/home/USERNAME/logs/job.%J.err
#SBATCH --output=/home/USERNAME/logs/job.%J.out

module load anaconda/4.6.11-py37
conda activate nf-core-rnaseq-1.4.2

echo "CONDA ENV : $CONDA_DEFAULT_ENV"
echo "Starting at `date`"
echo "Running on hosts: $SLURM_NODELIST"
echo "Running on $SLURM_NNODES nodes."
echo "Running $SLURM_NTASKS tasks."
echo "Current working directory is `pwd`"

# WORKS OK
# srun nextflow run nf-core/rnaseq -r 1.4.2 -profile test,conda

# WORKS OK
# srun nextflow run nf-core/rnaseq -r 1.4.2 -profile cuba,conda,cluster --genome GRCh37 -resume

# WORKS 80% - GRCh37 -> GRCh38, use --skipBiotypeQC switch to avoid error | https://bit.ly/3p8fhiN
# srun nextflow run nf-core/rnaseq -r 1.4.2 -profile cuba,conda,cluster --genome GRCh38 --skipBiotypeQC

srun nextflow run nf-core/rnaseq -r 1.4.2 -profile cuba,conda,cluster --genome GRCh38 --skipBiotypeQC -resume

srun echo "Finished Nextflow process"