auto_process_ngs.commands.update_fastq_stats_cmd
- auto_process_ngs.commands.update_fastq_stats_cmd.fastq_statistics(ap, stats_file=None, per_lane_stats_file=None, unaligned_dir=None, sample_sheet=None, name=None, add_data=False, force=False, nprocessors=None, runner=None)
Generate statistics for Fastq files
Generates statistics for all Fastq files found in the ‘unaligned’ directory, by running the ‘fastq_statistics.py’ program.
- Arguments
- ap (AutoProcessor): autoprocessor pointing to the analysis
directory to create Fastqs for
- stats_file (str): path of a non-default file to write the
statistics to (defaults to ‘statistics.info’ unless over-ridden by local settings)
- per_lane_stats_file (str): path for per-lane statistics
output file (defaults to ‘per_lane_statistics.info’ unless over-ridden by local settings)
- unaligned_dir (str): output directory for bcl-to-fastq
conversion
- sample_sheet (str): path to sample sheet file used in
bcl-to-fastq conversion
name (str): identifier to use for output stats files add_data (bool): if True then add stats to the existing
stats files (default is to overwrite existing stats files)
- force (bool): if True then force update of the stats
files even if they are newer than the Fastq files (by default stats are only updated if they are older than the Fastqs)
- nprocessors (int): number of cores to use when running
‘fastq_statistics.py’
- runner (JobRunner): (optional) specify a non-default job
runner to use for running ‘fastq_statistics.py’
- auto_process_ngs.commands.update_fastq_stats_cmd.get_absolute_file_path(p, base=None)
Get absolute path for supplied path
- Parameters:
p (str) – path
base (str) – optional, base directory to use if p is relative
- Returns:
absolute path for p.
- Return type:
String
- auto_process_ngs.commands.update_fastq_stats_cmd.report_processing_qc(ap, html_file, name=None, full_stats_file=None, per_lane_stats_file=None, per_lane_sample_stats_file=None)
Generate HTML report for processing statistics
- Parameters:
ap (AutoProcess) – AutoProcess instance to report the processing from
html_file (str) – destination path and file name for HTML report
name (str) – identifier to insert into report title
full_stats_file (str) – path of full stats file (defaults to ‘statistics_full.info’)
per_lane_stats_file (str) – path of per-lane statistics file (defaults to ‘per_lane_statistics.info’)
per_lane_sample_stats_file (str) – path of per-lane sample statistics file (defaults to ‘per_lane_sample_stats.info’)
- auto_process_ngs.commands.update_fastq_stats_cmd.update_fastq_stats(ap, sample_sheet=None, name=None, stats_file=None, per_lane_stats_file=None, unaligned_dir=None, add_data=False, force=False, nprocessors=None, runner=None)
Update statistics for Fastq files
Updates the statistics for all Fastq files found in the ‘unaligned’ directory, by running the ‘fastq_statistics.py’ program.
- Arguments
- ap (AutoProcessor): autoprocessor pointing to the analysis
directory to create Fastqs for
- sample_sheet (str): path to sample sheet file used in
bcl-to-fastq conversion (defaults to the sample sheet stored in the analysis directory parameters)
name (str): identifier to use for output stats files stats_file (str): path of a non-default file to write the
statistics to (defaults to ‘statistics.info’ unless over-ridden by local settings)
- per_lane_stats_file (str): path for per-lane statistics
output file (defaults to ‘per_lane_statistics.info’ unless over-ridden by local settings)
- unaligned_dir (str): output directory for bcl-to-fastq
conversion
- add_data (bool): if True then add stats to the existing
stats files (default is to overwrite existing stats files)
- force (bool): if True then force update of the stats
files even if they are newer than the Fastq files (by default stats are only updated if they are older than the Fastqs)
- nprocessors (int): number of cores to use when running
‘fastq_statistics.py’
- runner (JobRunner): (optional) specify a non-default job
runner to use for running ‘fastq_statistics.py’