Tidy up example

.gitlab-ci.yml

 # Run our tests against a specific version of astrocyte
 before_script:
-  - module load astrocyte/0.1.0
-
+  - module load astrocyte
 
 stages:
     - check

LICENSE.md

-Copyright © 2016. The University of Texas Southwestern Medical Center
+Copyright © 2019. The University of Texas Southwestern Medical Center
 5323 Harry Hines Boulevard Dallas, Texas, 75390 Telephone 214-648-3111
 

README.md

-# Example Wordcount Package
+# Example Ignite Wordcount Package
 
 [![Build
 Status](https://git.biohpc.swmed.edu/BioHPC/astrocyte_example_wordcount/badges/master/build.svg)](https://git.biohpc.swmed.edu/BioHPC/astrocyte_example_wordcount/commits/master)
-[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.1.0-blue.svg)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
+[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.2.0-blue.svg)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
 
-This is an example workflow package for astrocyte. It contains a worfklow
+This is a minimal test workflow package that counts the occurences of words
+in a test file. It can be used as a template to develop workflows, and as to
+test the astrocyte platform. This version uses the Ignite executor for
+Nextflow, so that processes all execute inside a single batch job allocation.
 to count the occurences of each word in a text file.
 
 ## The Workflow
 
 The workflow `workflow/main.nf` has three processes:
 
-  - Convert all the text in the input files to uppercase
-  - Split the text so each word is on a separate line
-  - Sort, find and count the occurence of unique words
+  - `parameters` outputs the parameters provided to the workflow, as an example
+    of how workflows receive the different types of parameters that can be setup
+    in the `astrocyte_pkg.yml` file.
+  - `uppercase` converts all the text in the input files to uppercase
+  - `tolines` splits the text so each word is on a separate line
+  - `wordcount` sorts, find and count the occurence of unique words
 
 ## Parameters
 
-There is a single parameter `story`. This provides 1 or more files that the
-workflow should run on.
+There is a single parameter which affects the workflow - `story`. This provides
+1 or more files that the workflow should run on.
+
+Additional parameters named `test_xxx` are included only to show how to define
+the parameter type in the `astrocyte_pkg.yml` file. They are simply printed to
+STDOUT by the workflow's `parameters` process.
+
+## Ignite Execution
+
+The workflow can be run using Nextflow + Apache Ignite using the `astrocyte_cli` tool. On the BioHPC cluster:
+
+```sh
+module add astrocyte
+astrocyte ignite-cluster astrocyte_example_wordcount_ignite
+```
+
+An example Slurm sbatch script `workflow/ignite_batch.sh` has been included to
+provide a template for running Nextflow workflows with Ignite outside of
+astrocyte.
+
+Both the `astrocyte_pkg.yml` and `ignite_batch.sh` are set so that the workflow
+will run using 4 x 32GB nodes on the BioHPC Nucleus cluster. The `tolines`
+process in the `main.nf` workflow has been artificially set to require 16 cpus,
+and sleep for 300s so that you can examine the running workflow to see how
+Ignite distributes jobs between nodes.
+
 
 ## Questions
 

astrocyte_pkg.yml

@@ -13,7 +13,7 @@ author: 'David Trudgian'
 # A contact email address for questions
 email: 'biohpc-help@utsouthwestern.edu'
 # A more informative title for the workflow package
-title: 'Example Wordcount Workflow'
+title: 'Ignite Example Wordcount Workflow'
 # A summary of the workflow package in plain text
 description: |
   This is a minimal test workflow package that counts the occurences of words