slurm_fuchs_workflow_paired.sh

#!/bin/bash

# @Author: Tobias Jakobi <tjakobi>
# @Email:  tobias.jakobi@med.uni-heidelberg.de
# @Project: University Hospital Heidelberg, Section of Bioinformatics and Systems Cardiology
# @License: CC BY-NC-SA

#SBATCH -n 1
#SBATCH -N 1
#SBATCH -c 40
#SBATCH --mem=200G
#SBATCH -J "FUCHS"
#SBATCH -p long
#SBATCH --mail-type=END,FAIL,TIME_LIMIT_80
#SBATCH --mail-user=tobias.jakobi@med.uni-heidelberg.de

# check if we have 3 arguments
if [ ! $# == 4 ]; then
  echo "Usage: $0 [Sample name] [target dir e.g. /path/to/data/] [BED file] [CircRNACount file]"
  exit
fi


main_out=$2/
sample_name=$1
bed_file=$3
dcc_file=$4
tmp_folder=/scratch/global_tmp/


#######################

main_bam=$sample_name/Aligned.noS.bam
main_junction=$sample_name/Chimeric.out.junction

mate1_bam=$sample_name/mate1/Aligned.sortedByCoord.out.bam
mate1_junction=$sample_name/mate1/Chimeric.out.junction

mate2_bam=$sample_name/mate2/Aligned.sortedByCoord.out.bam
mate2_junction=$sample_name/mate2/Chimeric.out.junction.fixed

merged_bam=$main_out/${1}_merged.bam

###################

# preprocessing

# merge both mate BAM files into one new BAM file
samtools merge -l 9 -@ 40 $merged_bam $main_bam $mate1_bam $mate2_bam

# re-index the newly aggregated BAM file
samtools index $merged_bam

FUCHS -N $sample_name -D $dcc_file -B $merged_bam -A $bed_file -O $main_out -F $mate1_junction -R $mate2_junction -J $main_junction -T $tmp_folder -r 4 -e 2 -q 2 -P 40