auto_process_ngs.commands.setup_analysis_dirs_cmd

auto_process_ngs.commands.setup_analysis_dirs_cmd.setup_analysis_dirs(ap, name=None, unaligned_dir=None, project_metadata_file=None, ignore_missing_metadata=False, short_fastq_names=False, link_to_fastqs=False, projects=None, undetermined_project=None)

Construct and populate project analysis directories

Parameters:

• unaligned_dir (str) – optional, name of ‘unaligned’ subdirectory (defaults to value stored in parameters)

• name (str) – (optional) identifier to append to output project directories

• project_metadata_file (str) – optional, name of the ‘projects.info’ metadata file to take project information from

• ignore_missing_metadata (bool) – if True then make project directories for all projects even if metadata hasn’t been set (default is to stop if metadata isn’t set)

• short_fastq_names (bool) – if True then use ‘short’ Fastq names (default is to use full Fastq names as output from bcl2fastq)

• link_to_fastqs (bool) – if True then make symbolic links to the Fastq files in the source ‘unaligned’ subdir (default is to make hard links)

• projects (list) – optional, subset of projects to create analysis dirs for (default is to attempt to create directories for all projects in the metadata file).

• undetermined_project (str) –

  optional, specify name for

  project directory to create with ‘undetermined’ Fastqs

  (defaults to ‘undetermined’)