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TOBIAS_snakemake/example_config.yaml

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#-------------------------------------------------------------------------#
#-------------------------- TOBIAS input data ----------------------------#
#-------------------------------------------------------------------------#
data:
Bcell: [data/Bcell_chr4.bam] #list of .bam-files
Tcell: [data/Tcell_chr4_*.bam] #list of .bam-files
run_info:
organism: human #mouse/human
fasta: data/genome_chr4.fa.gz #.fasta-file containing organism genome
blacklist: data/blacklist_chr4.bed #.bed-file containing blacklisted regions
gtf: data/genes_chr4.gtf #.gtf-file for annotation of peaks
motifs: data/individual_motifs/* #motifs (directory with files or individual files in MEME/JASPAR/PFM format)
output: test_output #output directory
#-------------------------------------------------------------------------#
#----------------------- Default module parameters -----------------------#
#-------------------------------------------------------------------------#
macs: "--nomodel --shift -100 --extsize 200 --broad"
atacorrect: ""
footprinting: ""
bindetect: ""