fix(appyter): Add hack to get example working

Co-authored-by:  sruthipsuresh <sps180004@utdallas.edu>

software/appyter/main.nf

@@ -19,17 +19,24 @@ process APPYTER {
     }
 
     input:
-    path input
+    path input_json
+    path input_files
 
     output:
-    path "data/output.ipynb", emit: output_notebook
-    path  "*.version.txt"   , emit: version
+    path "output.ipynb", emit: output_notebook
+    // TODO path  "*.version.txt"   , emit: version
 
     script:
     // Add soft-links to original FastQs for consistent naming in pipeline
     def software = getSoftwareName(task.process)
 
     """
-    appyter nbconstruct -i $input -o data/output.ipynb
+    CURRENTWORK=`pwd`
+    cp $input_json ~
+    cp $input_files ~
+    cd ~
+    appyter nbconstruct -i $input_json -o output.ipynb
+    appyter nbexecute output.ipynb
+    cp output.ipynb \$CURRENTWORK
     """
 }

tests/software/appyter/input.json

@@ -0,0 +1,7 @@
+{
+    "description": "testrun",
+    "number_1": 3,
+    "number_2": 5,
+    "operator": "add",
+    "file":     "test.txt"
+}

tests/software/appyter/main.nf

@@ -7,5 +7,6 @@ include { APPYTER } from '../../../software/appyter/main.nf' addParams( appyter_
 workflow test_appyter {
     def input = []
     input = file("${launchDir}/tests/software/appyter/input.json", checkIfExists: true)
-    APPYTER ( input )
+    input_file = file("${launchDir}/tests/software/appyter/test.txt", checkIfExists: true)
+    APPYTER ( input, input_file)
 }

tests/software/appyter/test.txt

@@ -0,0 +1 @@
+This is a test file..