Configuring Workflow Input elements
Workflow Input elements are the main element type for bringing data into a workflow. At least one such element must be present in a workflow. By default, when a workflow is launched, the workflow wizard will prompt for data to be selected from the Navigation Area, or for data files to be imported on-the-fly using any compatible importer.
Workflow Input elements support the input of CLC format data, raw NGS data formats, such as fastq and fasta format files, and some other formats. When launching the workflow, data outside CLC locations is selected by choosing the "Select files for on-the-fly import" option.
Like other workflow elements, Input elements can be configured to limit the options available when launching the workflow. See Basic configuration of workflow elements for more on locking and unlocking element options.
For information about configuring reference data inputs in workflows, see Reference data and workflows. The use of the "Workflow role" option, available in tool input channels and in Input elements where reference data is expected is described there. Information about launching workflows where workflow roles have been defined is described in Specifying reference data in the launch wizard.
Configuring import options
Selection of input data from the Navigation Area (already imported data) or import of raw data using on-the-fly import can be enabled or disabled in Input elements (figure 14.39).
When on-the-fly import is enabled, you can choose whether to offer a specific set of importers that can be used when the workflow is launched, and you can configure settings for those importers. On-the-fly import options are:
- Allow any compatible importer All compatible importers will be available when launching the workflow and all the options for each importer will be configurable.
- Allow selected importers Specify particular importers to be available when launching the workflow. Options for each selected importer can be configured by clicking on the Configure Parameters button.
Figure 14.39: Workflow Input elements support configuration of where data can be imported from, the Navigation Area and/or from disk, making use of of on-the-fly import. Options associated with specified importers can also be configured here.
On-the-fly import versus using workflow elements for specific importers
For importing data as the first step of a workflow, on-the-fly importer, as described above, is the most flexible and commonly used option. However, workflow input elements for specific NGS importers are also available.
Examples using each of these options are shown in figure 14.40. How these translate when launching the workflow is shown in figures 14.41 and 14.42. The relative merits of each option are outlined in table 14.1.
Figure 14.40: Raw data can imported as part of a workflow run in 2 ways. Left: Include an Input element. and use on-the-fly import. Right: Use a specific Import element. Here, the Illumina import element was included.
Figure 14.41: Launching a workflow with an Input element and choosing to select files to import on-the-fly.
Figure 14.42: Launching a workfow with a dedicated import element, in this case, an Illumina import element.
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Notes:
- The use of Iterate elements to run all or part of a workflow in batches is described in Running part of a workflow multiple times.
- Configuration options for NGS importers are described in Import high-throughput sequencing data.
Saving data imported on-the-fly
To save data elements created using on-the-fly import, connect a Save On-the-Fly Imports (
) element to the relevant Input element and connect an Output element to it (figure 14.43).
The Save On-the-Fly Imports element only acts on data imported using on-the-fly import. If input data is selected from a CLC File Location, this element has no effect.
Figure 14.43: Using this workflow, data imported on-the-fly would be saved as an output from the Save On-the-Fly Imports element.
A Save On-the-Fly Imports element is not needed when an Iterate element is connected to the Input element being used for on-the-fly import. In this situation, an Output element can be connected directly to the Iterate element (figure 14.44).
Figure 14.44: When an Iterate element is connected to an Input element, data imported on-the-fly can be saved by connecting an Output element to the Iterate element.
Subsections