# -*- coding: utf-8 -*-
#
#  This file is part of Sequana software
#
#  Copyright (c) 2016-2021 - Sequana Development Team
#
#  Distributed under the terms of the 3-clause BSD license.
#  The full license is in the LICENSE file, distributed with this software.
#
#  website: https://github.com/sequana/sequana
#  documentation: http://sequana.readthedocs.io
#
##############################################################################



#################################################################
# bcl2fastq
#
# :Parameters:
#
#   intensities are expected to be found in input_directory/Data/Intensities
#   Base call data are to be found in input_directory/Data/Intensities/BaseCalls
#
#   if merge_all_lanes is set to True, merged all lanes. This must be used with
#   NextSeq sequencers for instance.
#
general:
  input_directory: 

###################################################################################
#
#
#
# --ignore_missing_bcls: interpret missing *.bcl files as no call (N)
# --no-bgzf-compression: turn off BGZF compression for FASTQ files
# --barcode-mismatches:  number of allowed mismatches per index
# merge_all_lanes: if false, use the --no-lane-splitting option
bcl2fastq:
    threads: 4
    barcode_mismatch: 0
    samplesheet_file: 
    ignore_missing_bcls: true
    no_bgzf_compression: true
    options: ''
    merge_all_lanes: true