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#!/bin/sh
#SBATCH --account <group>
#SBATCH --qos <group>
#SBATCH --job-name rnaseq
#SBATCH --mail-type END,FAIL
#SBATCH --mail-user <email>
#SBATCH --nodes 1
#SBATCH --ntasks 1
#SBATCH --cpus-per-task=9
#SBATCH --mem=24g
#SBATCH --time=16:00:00
#SBATCH --output=rnaseq_%j.log
date
## Prepare environment --------------------------------------------------
# Load required modules
module load parallel hisat2/2.2.0 fastqc multiqc trim_galore samtools htseq
## Prepare reference files -------------------------------------------------
# Links for reference files
# Reference genome fasta (compressed gz)
# E.g., https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/115/GCF_000188115.4_SL3.0/GCF_000188115.4_SL3.0_genomic.fna.gz
export refgenome=""
# Annotation gtf for reference genome (compressed gz)
# E.g., https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/115/GCF_000188115.4_SL3.0/GCF_000188115.4_SL3.0_genomic.gtf.gz
export refannotation=""
# Name for reference genome
# E.g., Sly3_Heinz
export refname=""
# Domain: "prok" for prokaryotes and "euk" for eukaryotes
export refdomain="euk"
# Nunber of CPU for parallel processing, usually number of CPU available - 1, multiple of 8.
export ncpu=8
## Run the analysis
./bash_script.sh $refgenome $refannotation $refname $refdomain $ncpu