from_bam.yaml

# Own parameters will be loaded during snakefile executiuon as well and hence
# can be used in new/extended snakemake rules!
################################################################################
## General/Snakemake parameters, only used/set by wrapper or in Snakemake cmdl, but not in Snakefile
pipeline: chip-seq
configfile:
cluster_configfile:
local: true
max_jobs: 5
## workingdir need to be required DNA-mapping output dir, 'outdir' is set to workingdir internally
workingdir:
## preconfigured target genomes (mm9,mm10,dm3,...) , see /path/to/snakemake_workflows/shared/organisms/
## Value can be also path to your own genome config file!
genome:
## paired end data?
paired: true
## Bin size of output files in bigWig format
bw_binsize: 25
## type of bigwig file to create
bigWigType: both
## Median/mean fragment length, only relevant for single-end data (default: 200)
fragment_length: 200
verbose: false
# sampleSheet_DB
sampleSheet:
# window_size
window_size: 150
#### Flag to control the pipeline entry point
bam_ext: '.bam'
fromBam:
plot_format: png
################################################################################
# Call snakemake directly, i.e. without using the wrapper script:
#
# Please save a copy of this config yaml file and provide an adjusted config
# via '--configfile' parameter!
# example call:
#
# snakemake --snakefile /path/to/snakemake_workflows/workflows/ChIP-seq/Snakefile
#           --configfile /path/to/snakemake_workflows/workflows/ChIP-seq/defaults.yaml
#           --directory /path/to/outputdir
#           --cores 32
################################################################################