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# 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.
#

input_directory: /pasteur/projets/specific/Biomics/Data/current/NextSeq/200804_NB501291_0260_AHTT55BGXF/bcl

###################################################################################
#
#
#
# --ignore_missing_bcls: interpret missing *.bcl files as no call (N)
# --write-fastq-reverse-complement:  generate FASTQs containing reverse complements of actual data
# --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: /pasteur/projets/specific/Biomics/Data/current/NextSeq/200804_NB501291_0260_AHTT55BGXF/fastq/SampleSheet.csv
    output_directory: .
    ignore_missing_bcls: true
    no_bgzf_compression: true
    options: ''
    merge_all_lanes: true
    write_fastq_reverse_complement: false