DAC-RNAseq-pipeline/job.script.sh at master · Dartmouth-Data-Analytics-Core/DAC-RNAseq-pipeline · GitHub

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#!/bin/bash

# Name of the job
#SBATCH --job-name=RNAseq.preprocess

# Number of compute nodes
#SBATCH --nodes=1

# specify que to submit to (preempt1 only contains q10 DAC node)
#SBATCH --partition=standard

# specify account you are submitting from
#SBATCH --account=nccc

# Walltime (job duration)
#SBATCH --time=60:00:00

# Email address
#SBATCH --mail-user=XXXXXXXXX@dartmouth.edu

# Email notifications (comma-separated options: BEGIN,END,FAIL)
#SBATCH --mail-type=FAIL

#----- Source conda environment
source /optnfs/common/miniconda3/etc/profile.d/conda.sh
conda activate /dartfs/rc/nosnapshots/G/GMBSR_refs/envs/snakemake

#----- Make slurm logs folder
mkdir -p slurm_logs

#----- Call Snakemake
snakemake -s Snakefile  \
	--conda-frontend conda \
	--use-conda \
	--conda-prefix /dartfs/rc/nosnapshots/G/GMBSR_refs/envs/DAC-RNAseq-pipeline \
	--profile cluster_profile \
	--rerun-incomplete \
	--keep-going