Skip to content

Files

Latest commit

 

History

History
50 lines (41 loc) · 2.02 KB

folders.md

File metadata and controls

50 lines (41 loc) · 2.02 KB

Workflow folder structure

The default layout for the Snakemake working directory, i.e. the directory specified with the option --directory / -d when invoking snakemake, is standardized to ease navigating through the subfolders. In the following, the abbreviation WD is used to refer to that directory.

If you followed the CUBI recommendation and created your Snakemake WD with the init.py script from the workflow repository, the WD will have been created one level above the workflow repository location (where the init.py script resides).

Inside the WD, you find several subfolders ...

Users: continue reading here

The only subfolder relevant to you is called results/. This folder contains all important result files of the analysis, plus two special files (manifest* and run_config*) that you should never delete, but can ignore. The entire content of the results/ folder should be saved in a secure location (with backup). Deleting any other folder inside the WD does not affect your results, but may cause delays if the analysis run is changed or continued later on - so please be sure that the analysis is complete before deleting anything.

Developers: continue reading here

By convention, a pipeline must sort all data files into one of the following folders:

  • proc/: processing; intermediate/temp data files, not vital
  • results/: everything relevant to the client/user
    • automatically contains a copy of the sample sheet, the manifest file, and a dump of the run config
  • global_ref/: global reference files either loaded from reference containers or ex nihilo, i.e. references manually placed in the pipeline context
  • local_ref/: reference data local to the pipeline context, e.g. postprocessed files generated as part of the run
  • log/: target for Snakemake log: files
  • rsrc/: target for Snakemake benchmark: files

There are a few other standard directories defined that you must use if needed. See the Snakemake module workflow/rules/common/10_constants.smk for a complete list.