refactor: scaffolds samplesshet ica CDCgov#149

modules/local/scaffolds_samplesheet_check.nf

@@ -12,22 +12,19 @@ process SCAFFOLDS_SAMPLESHEET_CHECK {
     path "versions.yml", emit: versions
 
     script: // This script is bundled with the pipeline, in cdcgov/phoenix/bin/
-    // Adding if/else for if running on ICA it is a requirement to state where the script is, however, this causes CLI users to not run the pipeline from any directory.
-    if (params.ica==false) { ica = "" } 
-    else if (params.ica==true) { ica = "python ${workflow.launchDir}/bin/" }
-    else { error "Please set params.ica to either \"true\" if running on ICA or \"false\" for all other methods." }
     // define variables
     def container_version = "base_v2.1.0"
     def container = task.container.toString() - "quay.io/jvhagey/phoenix@"
+    def script = params.ica ? "python ${params.ica_path}/check_assembly_samplesheet.py" : "check_assembly_samplesheet.py"
     """
-    ${ica}check_assembly_samplesheet.py \\
+    ${script} \\
     $samplesheet \\
     samplesheet.valid.csv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version | sed 's/Python //g')
-        check_assembly_samplesheet.py: \$(${ica}check_assembly_samplesheet.py --version )
+        check_assembly_samplesheet.py: \$(${script} --version )
         phoenix_base_container_tag: ${container_version}
         phoenix_base_container: ${container} 
     END_VERSIONS