auto_process_ngs.commands.merge_fastq_dirs_cmd

auto_process_ngs.commands.merge_fastq_dirs_cmd.merge_fastq_dirs(ap, primary_unaligned_dir, output_dir=None, dry_run=False)

Combine multiple ‘unaligned’ output directories into one

This method combines the output from multiple runs of CASAVA/bcl2fastq into a single ‘unaligned’-equivalent directory.

Currently it operates in an automatic mode and should detect additional ‘unaligned’ dirs on its own.

Parameters:

  • ap (AutoProcessor) – autoprocessor pointing to the parent analysis directory

  • primary_unaligned_dir (str) – the ‘unaligned’ dir that data from from all others will be put into (relative path), unless overridden by ‘output_dir’ argument

  • output_dir (str) – optional, new ‘unaligned’ dir that will be created to hold merged data (relative path, defaults to ‘primary_unaligned_dir’)

  • dry_run (boolean) – if True then just report operations that would have been performed.