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:
<parameter-name>-inputUsed to specify data held in a CLC Server data location or to specify CLC format files in another location, e.g. AWS S3.When working with CLC format files in a remote location, e.g. AWS S3, you can provide these as input to workflows by specifying the URLs directly. For example:
clcserver <login parameters> -A <workflowname> \\--<parameter-name>-input s3://bucketname/path/to/myreads.clc<parameter-name>-import-commandUsed for on-the-fly import. The list of available importers is provided in the command information. One of these is then expected as the argument for this parameter. When using this option, you then also provide parameters relevant to the importer specified.
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:
- Each parameter name includes the name of the workflow element it is associated with and every element in a workflow has a unique name.
- If parameter names within a workflow element are identical, numbers are appended to those names for use with the CLC Server Command Line Tools. Although this ensures parameter names are unique, we recommend that when editing workflows, duplicate parameter names within a given workflow element are avoided to avoid confusion.