auto_process_ngs.commands.clone_cmd
- auto_process_ngs.commands.clone_cmd.clone(ap, clone_dir, copy_fastqs=False, exclude_projects=False)
Make a ‘clone’ (i.e. copy) of an analysis directory
Makes a functional copy of an existing analysis directory, including metadata and parameters, stats files, processing reports and project subdirectories.
By default the ‘unaligned’ directory in the new directory is simply a symlink from the original directory; set the ‘copy_fastqs’ to make copies instead.
- Arguments
- ap (AutoProcessor): autoprocessor pointing to the parent
analysis directory
- clone_dir (str): path to the new directory to create as a
clone (must not already exist).
- copy_fastqs (boolean): set to True to copy the Fastq files
(otherwise default behaviour is to make symlinks)
- exclude_projects (boolean): set to True to exclude any
projects from the parent analysis directory