Run the workflow on Terra

Import ncov WDL workflow from Dockstore

1. Setup a Terra account

2. Navigate to Dockstore: ncov:master

3. Top right corner, under Launch with, click on Terra

4. Under “Workflow Name” set a name, can also leave default ncov, and select your Destination Workspace in the drop down menu.

5. Click button IMPORT

6. In your workspace, click on the WORKFLOWS tab and verify that the imported workflow is showing a card

Upload your data files into Terra

1. Navigate to: https://app.terra.bio/#upload.

2. Select your workspace

3. At the top, hit the + button to “create a collection”

4. Within the collection, at bottom right, click + button to upload file, or drag and drop files to upload them.

5. Go back to your Terra Dashboard

6. Click on the DATA tab

7. On the left, under OTHER DATA, click Files and there should be an “uploads/” folder shown to the right

8. Click on “uploads/” to view your collection and verify that your files have been uploaded

Connect your data files to the WDL workflow

1. On the DATA tab, click on + next to the TABLES section to create a Data Table

2. Download the “sample_template.tsv” file

3. Create a tab delimited file similar to below:

entity:ncov_examples_id     metadata        sequences       configfile_yaml
example     gs://COPY_PATH_HERE/example_metadata.tsv        gs://COPY_PATH_HERE/example_datasets/example_sequences.fasta.gz
example_build               gs://COPY_PATH_HERE/example-build.yaml

4. Upload to Tables and you should get something like:

5. Navigate back to the Workflow tab, and click on your imported “ncov” workflow

6. Click on the radio button “Run workflow(s) with inputs defined by data table”

7. Under Step 1, select your root entity type ncov_examples from the drop down menu.

8. Click on SELECT DATA to select all rows

9. Most of the values will be blank but fill in the values below:

Task name	Variable	Type	Attribute
Nextstrain_WRKFLW	build_name	String	this.ncov_example.id
Nextstrain_WRKFLW	configfile_yaml	File	this.configfile_yaml
Nextstrain_WRKFLW	metadata_tsv	File	this.metadata
Nextstrain_WRKFLW	sequence_fasta	File	this.sequences

10. Click on the OUTPUTS tab

11. Connect your generated output back to the data table, but filling in values:

Task name	Variable	Type	Attribute
Nextstrain_WRKFLW	auspice_zip	File	this.auspice_zip
Nextstrain_WRKFLW	results_zip	File	this.results_zip

12. Click on Save then click on Run Analysis

13. Under the tab JOB HISTORY, verify that your job is running.

14. When run is complete, check the DATA / TABLES / ncov_examples tab and download “auspice.zip” file