Fix blank output file issue

astrocyte_pkg.yml

@@ -35,7 +35,7 @@ minimum_astrocyte_version: '0.4.1'
 # The Nextflow version that requires to run this workflow.  For old pipelines, which do not have this label 
 # a default value of 0.31.0 will be assigned automatically. Please make sure the requested nextflow version is available
 # in the module list.
-nextflow_version: '20.01.0'
+nextflow_version: '21.04.1'
 # (Optional) The Nextflow config file to use for this workflow. If provided, the file should exist in workflow/configs
 nextflow_config: 'biohpc.config'
 # The container to use for this workflow, none/singularity. If omitted, the default value 'none' will be used.
@@ -176,6 +176,8 @@ vizapp_r_module: 'R/3.6.1-gccmkl'
 # List of any CRAN packages, not provided by the modules, that must be made
 # available to the vizapp
 vizapp_cran_packages:
+  - shiny
+  - shinyFiles
   - plotly 
     
 # # List of any Bioconductor packages, not provided by the modules, that must be made

workflow/configs/biohpc.config

@@ -8,12 +8,12 @@ singularity {
 process {
     executor = 'local'
     withName:uppercase {
-        container = 'ubuntu:latest'
+        container = 'docker://ubuntu:latest'
     }
     withName:tolines {
-        container = 'ubuntu:latest'
+        container = 'docker://ubuntu:latest'
     }
     withName:wordcounts {
-        container = 'centos:centos8'
+        container = 'docker://centos:centos8'
     }
 }

workflow/main.nf

@@ -6,7 +6,7 @@
  * This is a minimal test workflow package that astrocyte tests can run against.
  *
  * @authors
- * David Trudgian <David.Trudgian@UTSouthwestern.edu>
+ * David Trudgian, Peng Lian, Devin OKelly
  *
  */
 
@@ -27,9 +27,13 @@ stories = Channel.fromPath( params.story )
 process parameters {
 
     cpus 1
-    //container 'ubuntu:latest'
 
     """
+    echo ""
+    echo "This script is running on:"
+    cat /etc/os-release
+    echo ""
+
     echo "Test Parameters Provided..."
     echo "story: ${params.story}"
     echo "test_int: ${params.test_int}"
@@ -37,9 +41,6 @@ process parameters {
     echo "test_string: ${params.test_string}"
     echo "test_select: ${params.test_select}"
     echo "test_multiselect: ${params.test_multiselect}"
-    pwd
-    whoami
-    env 
     """
 }
 
@@ -77,7 +78,6 @@ process tolines {
 
 process wordcounts {
 
-
     // Publish the outputs we create here into the workflow output directory
     publishDir "$baseDir/output", mode: 'copy'
 
@@ -88,6 +88,11 @@ process wordcounts {
     file "${wordlines.name}.wordcount"
 
     """
+    echo ""
+    echo "This script is running on:"
+    cat /etc/os-release
+    echo ""
+
     cat "$wordlines" | sort | uniq -c | sort -n -r > "${wordlines.name}.wordcount"
     """
 }