Make sure examples work, lots of wordsmithing and reorganizing for clarity.

[arvados.git] / 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 8dcb8e674e55021313dad6bd4cea1902e3187b9f..8a082257231196293c06bf2c6e3b5c879df6e3c7 100644 (file)
--- a/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
@@ -23,13 +23,15 @@ notextile. <div class="spaced-out">
 
 # Start from the *Workbench Dashboard*.  You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
 # Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> 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 *<i class="fa fa-fw fa-gear"></i> Tutorial bwa mem cwl* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> 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 <span class="btn btn-sm btn-primary">Choose</span> 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 <span class="caret"></span>* menu and select *All Projects*. Search for and select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference*. You will then see a list of files. Select *<i class="fa fa-fw fa-file"></i> 19-fasta.bwt* and click the <span class="btn btn-sm btn-primary" >OK</span> 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 <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> 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 <span class="label label-success">complete</span> label when the process completes successfully.
+# In the search box, type in *bwa-mem.cwl*.
+# Select *<i class="fa fa-fw fa-gear"></i> bwa-mem.cwl* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> 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 <span class="btn btn-sm btn-primary">Choose</span> button beneath the *read_p1* header.  This will open a dialog box titled *Choose a file*.
+# In the file dialog, click on *Home <span class="caret"></span>* menu and then select *All Projects*.
+# Enter *HWI-ST1027* into the search box.  You will see one or more collections. Click on *<i class="fa fa-fw fa-archive"></i>  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 <span class="btn btn-sm btn-primary" >OK</span> 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 <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> 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 <span class="label label-success">complete</span> 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 <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> download button to the right of the SAM file to download your results.