slurm-submit-script-WITHOUT-containers.sh
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slurm-submit-script-WITHOUT-containers.sh
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			#!/bin/bash

			#SBATCH --job-name=pipeline2-no-containers
			#SBATCH --partition=shi
			#SBATCH --time=02:00:00
			#SBATCH --cpus-per-task=4
			#SBATCH --mem=10G
			#SBATCH --output=no-containers.log

			module load Bowtie2/2.2.9-goolf-1.7.20
			module load SAMtools/1.3.1-goolf-1.7.20
			module load freebayes/1.1.0-goolf-1.7.20_39e5e4b

			# create output directories if they don't exist
			[ -d output/bowtie2 ] \|\| mkdir -p output/bowtie2
			[ -d output/samtools ] \|\| mkdir -p output/samtools
			[ -d output/freebayes ] \|\| mkdir -p output/freebayes


			RefGenome='./scicore-pipeline2-input-data/RefGenome/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/'

			echo 'aligning reads with bowtie2...'
			bowtie2 -p ${SLURM_CPUS_PER_TASK} -x $RefGenome/Bowtie2Index/genome -q -1 scicore-pipeline2-input-data/fastq/SRR5511076_1.ds.fastq -2 scicore-pipeline2-input-data/fastq/SRR5511076_2.ds.fastq -S output/bowtie2/yeast_reseq_ds-bt2aln.sam

			echo 'SAM to sorted BAM...'
			samtools view -bS output/bowtie2/yeast_reseq_ds-bt2aln.sam \| samtools sort - --threads ${SLURM_CPUS_PER_TASK} -o output/samtools/yeast_reseq_ds-bt2aln.s.bam
			#rm output/bowtie2/yeast_reseq_ds-bt2aln.sam

			echo 'calling variants with FreeBayes...'
			freebayes -f $RefGenome/WholeGenomeFasta/genome.fa output/samtools/yeast_reseq_ds-bt2aln.s.bam > output/freebayes/yeast_reseq_ds-bt2aln.s.vcf