* How to create a new pipeline from an existing template.
* How to browse and select input data for the pipeline and submit the pipeline to run on the Arvados cluster.
* How to access your pipeline results.
@@ -14,15 +14,17 @@ A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of s
notextile.
+h3. Steps
+
# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on * Dashboard* in the upper left corner of any Workbench page.
# Click on the Run a pipeline... button. This will open a dialog box titled *Choose a pipeline to run*.
-# Click to open the *All projects * menu. Under the *Projects shared with me* header, select * Arvados Tutorial*.
+# In the search box, type in *Tutorial align using bwa mem*.
# Select * Tutorial align using bwa mem* and click the Next: choose inputs button. This will create a new pipeline in your *Home* project and will open it. You can now supply the inputs for the pipeline.
-# The first input parameter to the pipeline is *Reference genoma (fasta)*. Click the Choose button beneath that header. This will open a dialog box titled *Choose a dataset for Reference genome (fasta)*.
-# Once again, open the *All projects * menu and select * Arvados Tutorial*. Select * Tutorial chromosome 19 reference* and click the OK button.
-# Repeat the previous two steps to set the *Input genome (fastq)* parameter to * Tutorial sample exome*.
+# The first input parameter to the pipeline is *"reference_collection" parameter for run-command script in bwa-mem component*. Click the Choose button beneath that header. This will open a dialog box titled *Choose a dataset for "reference_collection" parameter for run-command script in bwa-mem component*.
+# Open the *Home * menu and select *All Projects*. Search for and select * Tutorial chromosome 19 reference* and click the OK button.
+# Repeat the previous two steps to set the *"sample" parameter for run-command script in bwa-mem component* parameter to * Tutorial sample exome*.
# Click on the Run button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster.
-# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a complete label under the *job* column when the pipeline completes successfully.
+# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a complete label when the pipeline completes successfully.
# Click on the *Output* link to see the results of the job. This will load a new page listing the output files from this pipeline. You'll see the output SAM file from the alignment tool under the *Files* tab.
# Click on the download button to the right of the SAM file to download your results.