Executing workflows

Available workflows are listed when the clcserver command is run with the required information for logging in but without the -A flag specified. E.g.

clcserver -S <server> -U <username> -W <password or token>

Unlocked workflow parameters, i.e. those that can be configured, are listed when the clcserver command is run with the required information for logging in, and include -A flag followed by the workflow name.

clcserver -S <server> -U <username> -W <password or token> -A <workflow-name>

Workflows must be installed on the CLC Server for them to be available to launch using the CLC Server Command Line Tools.

Workflows are described in detail here: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Workflows.html

Running Template Workflows

Template workflows provided by CLC Workbenches, plugins and modules are not installed on the CLC Server by default. To launch such workflows using the CLC Server Command Line Tools, make a copy of the workflow, save that copy, and then install it on the CLC Server. Doing this is described at: https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Installing_configuring_workflows.htm.

Each input is specified using a dedicated parameter call

As with tools, each input to a workflow must be specified with its own parameter. Lists of input files as an argument to a single parameter are not accepted. For example, for 2 input elements, the general form would be:

--<parametername>-workflow-input <firstdataelement> --<parametername>-workflow-input <anotherdataelement>

On-the-fly import using the CLC Server Command Line Tools

For each workflow Input element, you either specify CLC data elements, or you specify on-the-fly import of data. On-the-fly import indicates that data should be imported as the first step taken when the workflow is run.

Configuring inputs in workflow designs, including on-the-fly import, is described in the CLC Genomics Workbench at http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Configuring_input_output_elements.html.

Parameters relating to a workflow input are listed when an incomplete command of the following form is run:

clcserver -S <servername> -U <username> -W <passwd-or-token> -A <workflowname>

For a workflow with a default configuration, these parameters would be:

Only one of these should be specified for a given workflow input.

An importer's parameters are listed when an incomplete command is run that contains the
<parameter-name>-import-command parameter with an importer name as the argument. For example, to see a list of parameters for use with the Illumina importer, a command of this form could be run:

clcserver -S<servername>-U <username>-W <passwd-or-token> -A <workflowname> \\
-<parameter-name>-import-command ngs_import_illumina

Each input file needs to be specified individually. E.g. when using the the Illumina importer to import 2 files, part of the command would look like:

-<parameter-name>-import-command ngs_import_illumina \\
--workflow-input-select-files clc://serverfile/full/path/to/impexpdir/reads/seq _R1.fastq \\
--workflow-input-select-files clc://serverfile/full/path/to/impexpdir/reads/seq1_R2.fastq

A list of input files is not accepted as the argument for input parameters.

Parameter names in workflows

The name of parameters within workflows are unique. This is ensured 2 ways: