13558: Merge branch 'master' into wtsi-hgi-13558-debug-log-tag-req-id

[arvados.git] / doc / user / composer / composer.html.textile.liquid

diff --git a/doc/user/composer/composer.html.textile.liquid b/doc/user/composer/composer.html.textile.liquid
index d6671013dd5322af013dbe84c1f43692788a6e0b..e8ef0b68858fa723265978638fce920ddfc803d8 100644 (file)
--- a/doc/user/composer/composer.html.textile.liquid
+++ b/doc/user/composer/composer.html.textile.liquid
@@ -9,7 +9,7 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-The Arvados Workflow Composer is a graphical interface for building Common Workflow Language (CWL) analysis workflows to run on Arvados.
+The Arvados Workflow Composer is a graphical interface for building Common Workflow Language (CWL) workflows to run on Arvados.
 
 This tutorial will demonstrate:
 
@@ -48,7 +48,7 @@ h3. 6. Create a new Command Line Tool
 
 h3. 7. Set Docker image, base command, and input port for "sort" tool
 
-You may need to "upload a Docker image":{{site.baseurl}}/user/topics/arv-docker.html (@arv-keepdocker debian:8@)
+The "Docker Repository" is the name:tag of a "Docker image uploaded Arvados.":{{site.baseurl}}/user/topics/arv-docker.html (Use @arv-keepdocker --pull debian:8@)  You can also find prepackaged bioinformatics tools on various sites, such as http://dockstore.org and http://biocontainers.pro/ .
 
 !(screenshot)c6.png!
 
@@ -60,48 +60,60 @@ h3. 9. Capture output file
 
 !(screenshot)c8.png!
 
-h3. 10. Repeat steps 6-9 for "uniq" tool
+h3. 10. Save Command Line Tool
 
-h3. 11. Create workflow
+!(screenshot)c22.png!
+
+h3. 11. Repeat steps 6-10 for "uniq" tool
+
+Create a new tool with a "base command" of "uniq".
+
+h3. 12. Switch back to "Home" tab and create workflow
+
+!(screenshot)c24.png!
 
 !(screenshot)c9.png!
 
 !(screenshot)c10.png!
 
-h3. 12. Drag and drop tools into Workflow
+h3. 13. Drag and drop tools into Workflow
 
 !(screenshot)c11.png!
 
-h3. 13. Drag and from input port of "sort" to empty space to create workflow input
+h3. 14. Drag from input port of "sort" to empty space to create workflow input
 
 !(screenshot)c21.png!
 
-h3. 14. Drag from output port of "sort" to input port of "uniq"
+h3. 15. Drag from output port of "sort" to input port of "uniq"
 
 !(screenshot)c13.png!
 
-h3. 15. Drag and from output port of "uniq" to empty space to create workflow output
+h3. 16. Drag from output port of "uniq" to empty space to create workflow output
 
 !(screenshot)c14.png!
 
-h3. 16. Click on "Test" tab then click "Run"
+h3. 17. Save Workflow
+
+!(screenshot)c23.png!
+
+h3. 18. Click on "Test" tab then click "Run"
 
 !(screenshot)c15.png!
 
-h3. 17. Choose input file
+h3. 19. Choose input file
 
 You may need to "upload an input file":{{site.baseurl}}/user/tutorials/tutorial-keep.html
 
 !(screenshot)c16.png!
 
-h3. 18. Run the workflow
+h3. 20. Run the workflow
 
 !(screenshot)c17.png!
 
-h3. 19. Monitor progress
+h3. 21. Monitor progress (may take several minutes)
 
 !(screenshot)c18.png!
 
-h3. 20. Get workflow output
+h3. 22. Get workflow output
 
 !(screenshot)c19.png!