auto_process_ngs.commands.setup_cmd

auto_process_ngs.commands.setup_cmd.setup(ap, data_dir, analysis_dir=None, sample_sheet=None, run_number=None, analysis_number=None, extra_files=None, unaligned_dir=None)

Set up the initial analysis directory

This does all the initialisation of the analysis directory and processing parameters

Parameters:

  • ap (AutoProcess) – autoprocessor pointing to the analysis directory to create Fastqs for

  • data_dir (str) – source data directory

  • analysis_dir (str) – corresponding analysis directory

  • sample_sheet (str) – name and location of non-default sample sheet file; can be a local or remote file, or a URL (optional, will use sample sheet from the source data directory if present)

  • run_number (str) – facility run number

  • analysis_number (str) – optional number assigned to the analysis to distinguish it from other processing or analysis attempts. If supplied then will be appended to the analysis directory name (unless a name is explicitly supplied via ‘analysis_dir’)

  • extra_files (list) – arbitrary additional files to copy into the new analysis directory; each file can be a local or remote file or a URL

  • unaligned_dir (str) – directory with existing Fastqs output from CASAVA or bcl2fastq2; if specified then Fastqs will be taken from this directory (optional)