Use channel to handle files

astrocyte_pkg.yml

@@ -13,7 +13,7 @@ author: 'Peng Lian, Erand Smakaj'
 # A contact email address for questions
 email: 'biohpc-help@utsouthwestern.edu'
 # A more informative title for the workflow package
-title: 'Example git Based Workflow'
+title: 'Example Git Based Workflow'
 # A summary of the workflow package in plain text
 description: |
   This is a minimal example that uses Astrocyte as a runner to run an existing workflow in a given git repo.
@@ -119,7 +119,7 @@ workflow_parameters:
       A parameter that need to be passed to the above command
 
   - id: parameter_nonopt
-    type: string
+    type: file
     required: false
     description: |
       A non-optinal parameter that need to be passed to the above command

workflow/main.nf

@@ -16,6 +16,8 @@ params.parameter1 = "A"
 params.parameter2 = "B"
 params.parameter_nonopt = "$baseDir/../test_data/mobydick.txt"
 
+// It's better to use a channel to handle the files
+inputfiles = Channel.fromPath( params.parameter_nonopt )
 
 process parameters {
 
@@ -43,12 +45,15 @@ process run_source {
     queue 'super'
     cpus 1
 
+    input:
+    file inputfile from inputfiles
+    
     output:
     file "astrocyte_run.out"
     file "astrocyte_run.err"
 
     """
     # run the program with received parameters
-    eval $baseDir/../workflow/external_repo/astrocyte_example_git_source__slave/${params.source_entrypoint} -p1 ${params.parameter1} -p2 ${params.parameter2} ${params.parameter_nonopt} 1> astrocyte_run.out 2> astrocyte_run.err
+    eval $baseDir/../workflow/external_repo/astrocyte_example_git_source__slave/${params.source_entrypoint} -p1 ${params.parameter1} -p2 ${params.parameter2} $inputfile 1> astrocyte_run.out 2> astrocyte_run.err
     """
 }
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