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Download widget within a workflow

Using the downloadURL widget to retrieve data

You can use the “downloadURL” widget in Bwb to download files from an external source (e.g., a Google Drive, website, or file transfer protocol (FTP) site) for use in a workflow. This is the mechanism that we use in all our example workflows. The user can double-click on the "downloadURL" widget to specify the URL where a file is located, as well as the directory where this file will be downloaded.

The following demo video explains the download widgets in our Salmon RNA-seq workflow from the Basic Training episode. This Salmon workflow uses example Arabidopsis datasets and is based on the tutorial described here: https://combine-lab.github.io/salmon/getting_started/. There are two download widgets in this workflow:

  • Download a reference transcriptome for Arabidopsis.
  • Download input sequence data from this 4-condition experiment [accession PRJDB2508].

In this video, we will demonstrate:

  1. How to edit input parameters in a widget.
  2. How to copy and paste in Bwb.
  3. Changing the input data to DRR016130 in the “downloadURL” widget
  4. Execute the modified workflow

The next demo video shows how you can download an example file from a public Google Drive. This public Google folder contains an example file representing NCBI generated RNA-seq counts data from GEO with accession number GSE164073

Exercise

Change the URL in the “downloadURL” widget to download another file from a Google folder of your choice

Note that retrieving files from a public Google Drive is a simple workaround for file transfer for the purpose of this workshop. Bwb provides more advanced methods for data transfer, which will be covered in upcoming episodes.

You can start from scratch by dragging the “downloadURL” widget from the Utilities category in the Tool Dock. Alternatively, you can simply modify the URL of an existing “downloadURL” widget in an example workflow.