Executed with slrum, fully containerized

.gitignore

@@ -3,3 +3,7 @@ workflow/*.html
 workflow/*.csv
 
 .history
+.nextflow.log
+*.img
+*.txt
+*.wordcount

astrocyte_pkg.yml

@@ -9,18 +9,14 @@
 # A unique identifier for the workflow package, text/underscores only
 name: 'example_wordcount'
 # Who wrote this?
-author: 'Peng Lian, Devin OKelly'
+author: 'Peng Lian'
 # A contact email address for questions
 email: 'biohpc-help@utsouthwestern.edu'
 # A more informative title for the workflow package
 title: '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
-  in a test file. It can be used as a template to develop workflows, and as to
-  test the astrocyte platform. Please note that start from publish version 
-  0.0.8 and test version 0.0.2, this workflow will only support Astrocyte 0.4.1
-  and above.
+  Fully containerized version, runs with BioHPC registry and slurm.
 
 #### New Features in Astrocyte 0.4.0 and above ####
 citation: |
@@ -62,13 +58,13 @@ documentation_files:
 # Remember - The workflow file is always named 'workflow/main.f'
 #            The workflow must publish all final output into $baseDir
 
-# A list of clueter environment modules that this workflow requires to run.
-# Specify versioned module names to ensure reproducability.
+# A list of cluster environment modules that this workflow requires to run.
+# Specify versioned module names to ensure reproducibility.
 workflow_modules:
   - Test
 
 # A list of container images requires to run this workflow.
-# Specify full path and version names to ensure reproducability.
+# Specify full path and version names to ensure reproducibility.
 # This keyword is required when 'container' is specified in Astrocyte 0.4.1 and above.
 # Singularity supports different registries, please specify the protocol to use.
 # Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
@@ -96,7 +92,7 @@ workflow_containers:
 # OPTIONAL INFORMATION
 #  default:   A default value for the parameter (optional)
 #  min:       Minium value/characters/files for number/string/files types
-#  max:       Maxumum value/characters/files for number/string/files types
+#  max:       Maximum value/characters/files for number/string/files types
 #  regex:     A regular expression that describes valid entries / filenames
 #
 # SELECT TYPE
@@ -175,7 +171,7 @@ workflow_parameters:
 #            The workflow must publish all final output into $baseDir
 
 # Name of the R module that the vizapp will run against
-# A containerized version is recommanded.
+# A containerized version is recommended.
 vizapp_r_module: 'R/4.1.1-img'
 
 # List of any CRAN packages, not provided by the modules, that must be made
@@ -191,7 +187,7 @@ vizapp_bioc_packages:
   -
 
 # # List of any packages to install from GitHub using devtools, that must be
-# made availavle to the vizapp
+# made available to the vizapp
 vizapp_github_packages:
   -
 

workflow/configs/biohpc.config

@@ -9,19 +9,21 @@ singularity {
 }
 
 process {
-    executor = 'local'
+    executor = 'slurm'
+    clusterOptions = '--hold --no-kill'
+    queue = 'super'
+
     withName:parameters {
-        // Path to the singularity image files. The prefix "file://images/singularity/" is the cacheDir folder 
-        // in the singularity settings. Please keep this prefix for the path of your singularity images
-        container = 'file://images/singularity/ubuntu-latest.img'
+        container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/biohpc/astrocyte_example_wordcount/ubuntu:latest'
     }
     withName:uppercase {
-        container = 'file://images/singularity/ubuntu-latest.img'
+        container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/biohpc/astrocyte_example_wordcount/ubuntu:latest'
     }
     withName:tolines {
-        container = 'file://images/singularity/ubuntu-latest.img'
+        container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/biohpc/astrocyte_example_wordcount/centos:centos8'
     }
     withName:wordcounts {
-        container = 'file://images/singularity/centos-centos8.img'
+        container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/biohpc/astrocyte_example_wordcount/centos:centos8'
     }
+
 }

workflow/main.nf

@@ -30,10 +30,15 @@ process parameters {
 
     """
     echo ""
-    echo "This script is running on:"
+    echo "This script is running on \$(hostname):"
+    echo ""
     cat /etc/os-release
     echo ""
 
+    echo "The ENV of this host is:"
+    env
+    echo ""
+
     echo "Test Parameters Provided..."
     echo "story: ${params.story}"
     echo "test_int: ${params.test_int}"