example_config.yaml

#-------------------------------------------------------------------------#
#-------------------------- TOBIAS input data ----------------------------#
#-------------------------------------------------------------------------#

data:
  Bcell: [data/Bcell.bam]       #list of .bam-files
  Tcell: [data/Tcell_day*.bam]  #list of .bam-files
  
run_info:
  organism: human                           #mouse/human/zebrafish (used for macs to set "--gsize"; alternatively, set --gsize in macs parameters below)
  fasta: data/genome.fa.gz                  #.fasta-file containing organism genome. NOTE: must be uncompressed .fa or bgzip compressed compatible with samtools
  blacklist: data/blacklist.bed             #.bed-file containing blacklisted regions
  gtf: data/genes.gtf                       #.gtf-file for annotation of peaks. NOTE: must be uncompressed .gtf
  motifs: data/individual_motifs/*          #motifs (directory with files or individual files in MEME/JASPAR/PFM format)
  output: test_output                       #output directory 
  #peaks: data/merged_peaks_annotated.bed   #optional; pre-calculated annotated peaks
  #peaks_header: data/merged_peaks_annotated_header.txt #optional; header for pre-calculated annotated peaks

#Flags for parts of pipeline to include/exclude (all are True by default)
flags:
  plot_comparison: True #True/False
  plot_correction: True
  plot_venn: True
  coverage: True
  wilson: True

#-------------------------------------------------------------------------#
#----------------------- Default module parameters -----------------------#
#-------------------------------------------------------------------------#

macs: "--nomodel --shift -100 --extsize 200 --broad"
atacorrect: ""
footprinting: ""
bindetect: ""