X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ae4948ee3a6e2d55a44a31272d1f67b669b0345f..3101fea587bc08e0f4f00a583d1d9e2c953417c1:/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid?ds=sidebyside diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid index 9373c9bb24..8dad6ab25e 100644 --- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid +++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid @@ -17,12 +17,12 @@ notextile.
# 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*. -# Select * Tutorial align using bwa mem* and click the Next: choose inputs button. This will load a new page where you will supply the inputs for the pipeline. +# 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*. # 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 success label under the *job* the 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 under the *job* column 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.