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