#! /bin/bash -l
#SBATCH -A b2015155
#SBATCH -M milou
#SBATCH -p core -n 16
#SBATCH -t 1-00:00:00
#SBATCH -J mRNAmappingPipeline_TRAP
#SBATCH -e /proj/b2015155_nobackup/private/TRAP/reports/mRNAmappingPipeline_TRAP_SLURM_Job_id_%j.stderr.txt
#SBATCH -o /proj/b2015155_nobackup/private/TRAP/reports/mRNAmappingPipeline_TRAP_SLURM_Job_id_%j.stdout.txt
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=john.doe@scilifelab.se
cd /pica/v10/b2015155_nobackup/private/TRAP
# ==============================================================================
# LOADING MODULES
module load bioinfo-tools
# modules for mapping
module load star/2.4.1c
module load samtools
module load subread/1.5.0
module use /proj/b2013006/sw/modules
module load snakemake
# modules for qc
module load FastQC/0.11.2
module load multiQC/v.0.2
module load rseqc/2.6.2
module load ucsc-utilities
# Go to the working directory
cd /pica/v10/b2015155_nobackup/private/TRAP
# RUNNING SNAKEMAKE MAPPING SCRIPT WITH 16 cores
snakemake -j 16 -s scripts/RNAmappingPipeline/SnakeMakeFiles/mappingReads.sm