Update the documentation to include the new process.

README.md

@@ -13,6 +13,7 @@ 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
+- Remove all the empty lines generated from the split
 - Sort, find and count the occurrence of unique words
 
 This example uses SLURM to finish the calculation tasks. It may be slow due to the workload of the SLURM on BioHPC.
@@ -70,7 +71,7 @@ The `workflow_containers` section in `astrocyte_pkg.yml` defines the URL of the
 When the `astrocyte_cli` run this workflow, it will pull the images in this section and save them to
 `workflow/images/singularity/` for later use. In the workflow, the default configuration located in
 `workflow/configs/biohpc.config` defines how the Nextflow command to use the singularity executor for the uppercase,
-toLines, and word count processes.
+toLines, cleanlines, and word count processes.
 
 ### Vizapp containers
 

docs/index.md

@@ -5,10 +5,11 @@ in a text file.
 
 ## The Workflow
 
-The workflow `workflow/main.nf` has three processes:
+The workflow `workflow/main.nf` has four processes:
 
 - Convert all the text in the input files to uppercase
 - Split the text so each word is on a separate line
+- Remove all empty lines generated from the previous output
 - Sort, find and count the occurrence of unique words
 
 This example uses SLURM to finish the calculation tasks. It may be slow due to the workload of the SLURM on BioHPC.
@@ -63,10 +64,10 @@ astrocyte_cli viz astrocyte_example_wordcount
 ### Astrocyte workflow containers
 
 The `workflow_containers` section in `astrocyte_pkg.yml` defines the URL of the containers used by this workflow.
-When the `astrocyte_cli` run this workflow, it will pull the images in this section and save them to
+When the `astrocyte_cli` runs this workflow, it will pull the images in this section and save them to
 `workflow/images/singularity/` for later use. In the workflow, the default configuration located in
-`workflow/configs/biohpc.config` defines how the Nextflow command to use the singularity executor for the uppercase,
-toLines, and word count processes.
+`workflow/configs/biohpc.config` defines how the Nextflow command will use the singularity executor for the uppercase,
+toLines, cleanlines, and word count processes.
 
 ### Vizapp containers
 

workflow/main.nf

@@ -12,7 +12,7 @@
 
 // Path to an input file, or a pattern for multiple inputs
 // Note - $baseDir is the location of this workflow file main.nf
-params.story = "$baseDir/../test_data/mobydick.txt"
+params.story = "$baseDir/../test_data/*.txt"
 
 // Parameters for test values, only used for demonstrating parameter types
 params.test_int = 999