# ============================================================================
# Config file for coverage pipeline
# ==========================================[ Sections for the users ]========
#
# One of input_directory, input_pattern and input_samples must be provided
# If input_directory provided, use it otherwise if input_pattern provided,
# use it, otherwise use input_samples.
# ============================================================================
input_directory: "%(input_directory)s"
input_readtag: "%(input_readtag)s"
input_pattern: "%(input_pattern)s"

##############################################################################
#
# :Parameters:
#
# :param circular: is your genome circular or not ?
# :param double_threshold: double threshold for clustering. Keep 0.5 if you do
#     not know. Otherwise, checkout the online documentation on
#     sequana.readthedocs.io
# :param genbank_file: optional genbank 
# :param high_threshold:
# :param low_threshold:
# :param mixture_models: keep to 2.
# :param reference_file: optional fasta file corresponding to you mapped data. Used for
#     GC plot only
# :param window: the W parameter of the running median. Keep as long as twice
#     the deleted/depleted/duplicated you want to identify or to avoid. short
#     genome will be set to genome length divided by 5 automatically. 
# :param chunksize: for large genomes, split the data into chunks
# :param binning: for large genomes, merge data into bins of this size. You will
#     loose resolution: bins are merged and averaged indeed
# :param cnv_clustering: further clustering to merge detected events whose
#     distance is smaller than this parameter
#
coverage:
    circular: True
    window_size: 20001
    binning: -1
    cnv_clustering: -1
    chunksize: 5000000
    double_threshold: 0.5
    gc_window_size: 201
    annotation_file:
    high_threshold: 4.
    low_threshold: -4.
    mixture_models: 2
    reference_file: