X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/44c95f99098fa6c6acbfa82d4b6cbc6015eb6e39..438c1957f41643650b9a54419179c9228cd6fa6c:/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid diff --git a/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid index 6785ed68d9..8a08225723 100644 --- a/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid +++ b/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid @@ -19,14 +19,20 @@ A "workflow" (sometimes called a "pipeline" in other systems) is a sequence of s h3. Steps +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 process... button. This will open a dialog box titled *Choose a pipeline or workflow to run*. -# In the search box, type in *Tutorial bwa mem cwl*. -# Select * Tutorial bwa mem cwl* and click the Next: choose inputs button. This will create a new process in your *Home* project and will open it. You can now supply the inputs for the process. Please note that all required inputs are populated with default values and you can change them if you prefer. -# For example, let's see how to change *"reference" parameter* for this workflow. Click the Choose button beneath the *"reference" parameter* header. This will open a dialog box titled *Choose a dataset for "reference" parameter for cwl-runner in bwa-mem.cwl component*. -# Open the *Home * menu and select *All Projects*. Search for and select * Tutorial chromosome 19 reference*. You will then see a list of files. Select * 19-fasta.bwt* and click the OK button. -# Repeat the previous two steps to set the *"read_p1" parameter for cwl-runner script in bwa-mem.cwl component* and *"read_p2" parameter for cwl-runner script in bwa-mem.cwl component* parameters. -# Click on the Run button. The page updates to show you that the process has been submitted to run on the Arvados cluster. -# After the process starts running, you can track the progress by watching log messages from the component(s). This page refreshes automatically. You will see a complete label when the process completes successfully. +# In the search box, type in *bwa-mem.cwl*. +# Select * bwa-mem.cwl* and click the Next: choose inputs button. This will create a new process in your *Home* project and will open it. You can now supply the inputs for the process. Please note that all required inputs are populated with default values and you can change them if you prefer. +# For example, let's see how to set read pair *read_p1* and *read_p2* for this workflow. Click the Choose button beneath the *read_p1* header. This will open a dialog box titled *Choose a file*. +# In the file dialog, click on *Home * menu and then select *All Projects*. +# Enter *HWI-ST1027* into the search box. You will see one or more collections. Click on * HWI-ST1027_129_D0THKACXX for CWL tutorial* +# The right hand panel will list two files. Click on the first one ending in "_1" and click the OK button. +# Repeat the steps 5-8 to set the *read_p2* except selecting the second file ending in "_2" +# Scroll to the bottom of the "Inputs" panel and click on the Run button. The page updates to show you that the process has been submitted to run on the Arvados cluster. +# Once the process starts running, you can track the progress by watching log messages from the component(s). This page refreshes automatically. You will see a complete label when the process completes successfully. # Click on the *Output* link to see the results of the process. This will load a new page listing the output files from this process. 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. + +notextile.