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8 Invoking guix workflow

The Guix Workflow Language extends your Guix installation with a new sub-command: guix workflow. Here are some of the options the command accepts:

--input=name[=file]
-i name[=file]

A workflow may have so-called free inputs, inputs that are not provided by any of the workflow’s processes. By default, the GWL will pick files from the current working directory that match the names of free inputs. This option can be used to map a file with an arbitrary name to a free input in the workflow with the given name. This option can be provided more than once.

In the following example, the free input called genome is mapped to the file /data/hg19.fa before running the workflow defined in analysis.w:

guix workflow --input=genome=/data/hg19.fa --run=analysis.w
--output=location
-o location

This option currently has no effect.

--engine=engine
-e engine

Select the process engine engine as the target of the generated process scripts. See Process Engines.

--prepare=file
-p file

Generate the process scripts and build or download all dependencies, but do not run the workflow process scripts corresponding to the workflow defined in file.

--run=file
-r file

Generate the process scripts, build or download all dependencies, and then run the workflow process scripts corresponding to the workflow defined in file.

--dry-run
-n

Prepare the scripts and the environments but don’t actually run the processes. Only show what commands would be run.

--force
-f

Execute all processes, even if their outputs may have been cached from previous runs.

--container
-c

Run each process inside of an isolated environment with file system virtualization and user namespaces. Only declared input files will be available at execution time, and only declared output files will be stored. This is a great option to use when you want to make sure that your processes only depend on state that you have declared. A downside is that generated output files cannot be written to the target directories directly but are copied from the container to the file system.

--graph=file
-g file

Load the workflow file and generate a graph in Dot-format.

--web-interface
-w

The GWL includes a web interface. This option starts it.


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