Launch analysis using workflows

A guide to applying workflows to define parameters for your group's analyses

To upload your file or files, you can click on Upload/view files on the top of your screen, and then click on Select file(s).

You can also connect your Illumina BaseSpace account.

To create your samples you need to navigate through:

Manage > Samples > Create new samples

You can then define which files are associated with which sample name and you can optionally attach additional information to the sample (e.g phenotypes).

Note: FASTQ files are grouped according to the Illumina or MGI naming convention and are given a suggested sample name. The suggested name and associated files can be modified in the following screen. For VCF files - each VCF is associated with a suggested sample name.

Manage > Samples > Create new samples > Next: for adding more information to the sample, notes, phenotype, etc.

Create a workflow 

Only the group supervisor is capable of editing each workflow’s parameters. To do that, the group supervisor must navigate to: Manage > Workflows > Create workflows > Add new

You can use the locks to set fixed values in the workflow field

Then navigate to Launch analysis > New analysis. You can select an existing workflow from the dropdown.

Note: Group supervisor can disable the “launch analysis without a workflow” option in “Analysis preferences”

(Optional) define filters and sub analyses to reduce manual steps

You can specify which filters you would like to launch once the analysis is complete as part of the workflow.

You can launch an analysis using an existing workflow. Analyses parameters are loaded as defined in the workflow by the group supervisor. Some fields may be fixed if the supervisor has locked them. Other fields may have a default value (defined by the supervisor) but can be modified.