Command Line Interface

The CLI is able to process data from mzML through MS1 and MS2 peakpicking. For usage overview, simply invoke deimos --help or -h. A Snakemake configuration file in YAML format is required. DEIMoS will try to find config.yaml in the current directory, else a configuration file must be specified through the --config flag. A default workflow configuration (workflows/default_config.yaml) is provided, but this is intended to be modified and supplied by the user to accomodate workflow-specific needs.

$ deimos --help
usage: deimos [-h] [-v] [--config PATH] [--dryrun] [--unlock] [--touch]
              [--latency N] [--cores N] [--count N] [--start IDX]
              [--cluster PATH] [--jobs N]

DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry

optional arguments:
  -h, --help      show this help message and exit
  -v, --version   print version and exit
  --config PATH   path to yaml configuration file
  --dryrun        perform a dry run
  --unlock        unlock directory
  --touch         touch output files only
  --latency N     specify filesystem latency (seconds)
  --cores N       number of cores used for execution (local execution only)
  --count N       number of files to process (limits DAG size)
  --start IDX     starting file index (for use with --count)

cluster arguments:
  --cluster PATH  path to cluster execution yaml configuration file
  --jobs N        number of simultaneous jobs to submit to a slurm queue

Inputs (.mzML or .mzML.gz) will automatically be detected in the input/ folder, and results will be populated in a corresponding output/ folder, both relative to the current working directory. For example:

.
├── config.yaml
├── input
│  ├── example1.mzML.gz
│  ├── example2.mzML.gz
│  └── ...
└── output

For running in cluster environments, please consult the Snakemake workflow management system documentation concerning profiles.