positional arguments:

sample_sheet

The sample sheet containing sample data in CSV format.

optional arguments:

-h, --help

show this help message and exit

-v, --version

show program's version number and exit

--init [{settings,sample-sheet,both}]

Generate a template SETTINGS file, a SAMPLE-SHEET. Leave empty for both.

-s SETTINGS, --settings SETTINGS

A YAML file for settings that deviate from the defaults.

-c CONFIGFILE, --configfile CONFIGFILE

The config file used for calling the underlying snakemake process. By default the file 'config.json' is dynamically created from the sample sheet and the settings file.

--target TARGET

Stop when the named target is completed instead of running the whole pipeline. The default target is "final-report". Pass "--target=help" to describe all available targets.

-n, --dry-run

Only show what work would be performed. Do not actually run the pipeline.

--graph GRAPH

Output a graph in Graphviz dot format showing the relations between rules of this pipeline. You must specify a graph file name such as "graph.pdf".

--force

Force the execution of rules, even though the outputs are considered fresh.

--reason

Print the reason why a rule is executed.

--unlock

Recover after a snakemake crash.

This pipeline was developed by the Akalin group at MDC in Berlin in 2017-2018.

Version: 0.0.9