text: # User specific details
  mail = 'm.elferink@umcutrecht.nl'	#Email adress
  project = 'compgen'			#Project name for Slurm cluster
  
  # Paths to scripts
  repo_path = "/hpc/compgen/tools/Cyclomics_consensus_pipeline/"
  venv = str(repo_path)+ "venv/bin/activate"
  # Don't touch, should always be the same:
  default_slurm = repo_path + "run_dagcon_consensus.py"
  repeat_slurm = repo_path + "bin_on_repeat_count.py"
  default_nocluster = repo_path + "run_dagcon_consensus_nocluster.py"
  repeat_nocluster = repo_path + "bin_on_repeat_count_nocluster.py"
  split = repo_path + "split_forward_reverse_reads.py"
  calculate = repo_path + "calculate_depth.py"
  plot_dashboard = repo_path + "plot_Dashboard.R"
  check_numbers = repo_path + "check_numbers.py"
  find_read_bam = repo_path + "find_read_bam.py"
  structure = repo_path + "make_structure.py"
  cosmic = repo_path + "data_files/COSMIC_mutations.bed"
  lastparam = repo_path + "data_files/last_params"
  
  
  # Paths to tools
  bwa = "/hpc/local/CentOS7/cog_bioinf/bwa-0.7.17/bwa"
  sambamba = "/hpc/local/CentOS7/cog/software/sambamba-0.6.5/sambamba"
  bam2m5 = "/hpc/compgen/tools/bam2m5/bam2m5.py"
  pbdagcon = "/hpc/compgen/tools/pbdagcon/src/cpp/pbdagcon"
  lastal = "/hpc/compgen/tools/last-921/src/lastal"
  lastsplit = "/hpc/compgen/tools/last-921/src/last-split"
  mafconvert = "/hpc/compgen/tools/last-921/scripts/maf-convert"
  rscript= "/hpc/local/CentOS7/common/lang/R/3.2.2/bin/Rscript"
  samtools = "/hpc/local/CentOS7/cog/software/samtools-1.2/samtools"
  
  # Reference Genome files 
  full_ref = "/hpc/compgen/GENOMES/Cyclomics_reference_genome/version12/Homo_sapiens.GRCh37.GATK.illumina_cyclomics_backbone.fasta"
  target_ref = "/hpc/compgen/GENOMES/Cyclomics_reference_genome/version12/BRAF_TP53_EGFR_BB_pjet.fasta"
  
  
  #  General settings
  SLURM_JOB_TIME_SHORT = "4:00:00"        # Job time SLURM
  SLURM_JOB_TIME_MED = "144:00:00"        # Job time SLURM
  SLURM_JOB_TIME_LONG = "196:00:00"       # Job time SLURM
  
  MAX_MEM_TARGET = 12			# Memory SLURM (low for targeted mapping) 
  MAX_MEM_FULL  = 32 			# Memory SLURM (higher for full mapping)
  THREADS = 2 				# Threads to be used in several jobs
  MIN_CONS_LEN = 35			# Minimum consensus lenght for pbdagcon
  TRIM = 0				# Trim x basepairs from consensus pbdagcon
  BWA_MEM = "{bwa} mem -t 2 -c 100 -M -R".format(bwa=bwa)	# settings for BWA-mem
  MAX_READS_JOB_PLOT = 50000  		# Maximum reads in strucure plot. Note that this number must be lower tham the total reads in the analyses.
  
  #run_dagcon_consensus.py specific settings
  DAGCON_MIN_COV = 10			# Minimum coverage needed for consensus calling with pbdagcon
  SLURM_PARALLEL_JOBS = 200		# Maximum number of parallel jobs 
  MAX_READS_JOB = 1000			# Number of reads per jobs 
  
  #split_forward_reverse_reads.py specific settings
  SPLIT_MIN_PERC = 50 			# Minimal percentage to determine either forward or reverse mapped insert/backbone (50% = majority vote)
  STATES = ["forward","reverse"]		# States of mapping.
  
  #bin_on_repeat_count.py specific settings
  INSERT = "TP53"				# Dedault locus to be considered in-target
  PBDAGCON_PARAM = " -c 1 -t 0 -j 2 "	# pbdagcon settings
  MAX_FILE_COUNT = 0			# Maximum number of files used in bin repeat. This might be helpful with large runs that will take a very long time if all data is used. default 0 = off
  
  #make_structure.py specific settings
  STRUCTURE_OVERLAP = 100			# Overlap in bp to determine if insert fragements are from the same molecule/amplicon
  STRUCTURE_FLANK = 30			# Flank to determine unmapped regions to either BB or I
  STRUCTURE_MAD = 100			# If MAD score for insert startsite is more than threshold, report threshold
  STRUCTURE_INTARGET = "17:7565097-7590856"	# default repeat loci considered insert target
  
  