auto_process_ngs.bcl2fastq.apps

Provides methods to create Command instances for command line applications used in Bcl to Fastq conversion.

The following functions are available:

  • configureBclToFastq

  • bcl2fastq2

  • bclconvert

auto_process_ngs.bcl2fastq.apps.bcl2fastq2(run_dir, sample_sheet, output_dir='Unaligned', mismatches=None, bases_mask=None, ignore_missing_bcls=False, no_lane_splitting=False, minimum_trimmed_read_length=None, mask_short_adapter_reads=None, create_fastq_for_index_reads=False, find_adapters_with_sliding_window=False, loading_threads=None, demultiplexing_threads=None, processing_threads=None, writing_threads=None, bcl2fastq_exe=None)

Generate Command instance for ‘bcl2fastq’ program (v2.*)

Creates a Command instance to run the Illumina ‘bcl2fastq’ program (for versions 2.*).

Parameters:

  • run_dir – path to the top-level directory for the run

  • sample_sheet – path to the sample sheet file to use

  • output_dir – optional, path to the output directory. Defaults to ‘Unaligned’

  • mismatches – optional, specify maximum number of mismatched bases allowed for matching index sequences during multiplexing. Recommended values are zero for indexes shorter than 6 base pairs, 1 for indexes of 6 or longer (If not specified and bases_mask is supplied then mismatches will be derived automatically from the bases mask string)

  • bases_mask – optional, specify string indicating how to treat each cycle within each read e.g. ‘y101,I6,y101’

  • ignore_missing_bcls – optional, if True then interpret missing bcl files as no call (default is False)

  • no_lane_splitting – optional, if True then don’t split FASTQ files by lane (–no-lane-splitting) (default is False)

  • minimum_trimmed_read_length – optional, specify minimum length for reads after adapter trimming (shorter reads will be padded with Ns to make them long enough)

  • mask_short_adapter_reads – optional, specify the minimum length of ACGT bases that must be present in a read after adapter trimming for it not to be masked completely with Ns.

  • create_fastq_for_index_reads – optional, if True then also create Fastq files for index reads (default, don’t create index read Fastqs) (–create-fastq-for-index-reads)

  • find_adapters_with_sliding_window – optional, if True then use the sliding window algorithm rather than string matching when identifying adapter sequences for trimming (default, don’t use sliding window algorithm) (–find-adapters-with-sliding-window)

  • loading_threads – optional, specify number of threads to use for loading bcl data (–loading-threads)

  • demultiplexing_threads – optional, specify number of threads to use for demultiplexing (–demultiplexing-threads)

  • processing_threads – optional, specify number of threads to use for processing (–processing-threads)

  • writing_threads – optional, specify number of threads to use for writing FASTQ data (–writing-threads)

  • bcl2fastq_exe – optional, if set then specifies the name/path of the bcl2fastq executable to use

Returns:

Command object.

auto_process_ngs.bcl2fastq.apps.bclconvert(run_dir, output_dir, sample_sheet=None, lane=None, no_lane_splitting=False, sampleproject_subdirectories=False, num_parallel_tiles=None, num_conversion_threads=None, num_compression_threads=None, num_decompression_threads=None, bclconvert_exe=None)

Generate Command instance for ‘bcl-convert’ program (v3.*)

Creates a Command instance to run the Illumina ‘bcl-convert’ program (for versions 3.*).

Parameters:

  • run_dir – path to the top-level directory for the run

  • output_dir – path to the output directory

  • sample_sheet – optional, path to the sample sheet file to use (must be present in top-level of input directory if not specified here)

  • lane (integer) – restrict processing to single lane (sample sheet must only contain this lane) (–bcl-only-lane)

  • no_lane_splitting – optional, if True then don’t split FASTQ files by lane (–no-lane-splitting) (default is False)

  • sampleproject_subdirectories – optional, if True then create subdirectories with project names in output (default is False) (–bcl-sampleproject-subdirectories)

  • num_parallel_tiles – optional, specify the number of tiles being converted to Fastqs in parallel (–bcl-num-parallel-tiles)

  • num_conversion_threads – optional, specify the number of threads to use for conversion per tile (–bcl-num-conversion-threads)

  • num_compression_threads – optional, specify the number of threads for compressing output Fastq files (–bcl-num-compression-threads)

  • num_decompression_threads – optional, specify the number of threads for decompression input bcl files (–bcl-num-decompression-threads)

  • bclconvert_exe – optional, if set then specifies the name/path of the bcl-convert executable to use

Returns:

Command object.

auto_process_ngs.bcl2fastq.apps.configureBclToFastq(basecalls_dir, sample_sheet, output_dir='Unaligned', mismatches=None, bases_mask=None, force=False, ignore_missing_bcl=False, ignore_missing_stats=False, ignore_missing_control=False, configure_bcl_to_fastq_exe=None)

Generate Command instance for ‘configureBclToFastq.pl’ script

Creates a Command instance to run the CASAVA ‘configureBclToFastq.pl’ script (which generates a Makefile to perform the bcl to fastq conversion).

Parameters:

  • basecalls_dir – path to the top-level directory holding the bcl files (typically ‘Data/Intensities/Basecalls/’ subdirectory)

  • sample_sheet – path to the sample sheet file to use

  • output_dir – optional, path to the output directory. Defaults to ‘Unaligned’. If this directory already exists then the conversion will fail unless the force option is set to True

  • mismatches – optional, specify maximum number of mismatched bases allowed for matching index sequences during multiplexing. Recommended values are zero for indexes shorter than 6 base pairs, 1 for indexes of 6 or longer (If not specified and bases_mask is supplied then mismatches will be derived automatically from the bases mask string)

  • bases_mask – optional, specify string indicating how to treat each cycle within each read e.g. ‘y101,I6,y101’

  • force – optional, if True then force overwrite of an existing output directory (default is False)

  • ignore_missing_bcl – optional, if True then interpret missing bcl files as no call (default is False)

  • ignore_missing_stats – optional, if True then fill in with zeroes when *.stats files are missing (default is False)

  • ignore_missing_control – optional, if True then interpret missing control files as not-set control bits (default is False)

  • configure_bcl_to_fastq_exe – optional, if set then will be taken as the name/path for the ‘configureBclToFastq.pl’ script

Returns:

Command object.