refactor: ica handling CDCgov#149

main.nf

@@ -49,6 +49,7 @@ workflow PHOENIX {
     //input on command line
     if (params.input) { ch_input = file(params.input) } else { exit 1, 'For -entry PHOENIX: Input samplesheet not specified!' }
     ch_versions = Channel.empty() // Used to collect the software versions
+    if (params.ica != true && params.ica != false) {exit 1, "Please set params.ica to either \"true\" if running on ICA or \"false\" for all other methods."}
 
     main:
         PHOENIX_EXTERNAL ( ch_input, ch_versions, true )

modules/local/samplesheet_check.nf

@@ -12,22 +12,19 @@ process 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_samplesheet.py" : "check_samplesheet.py"
     """
-    ${ica}check_samplesheet.py \\
+    ${script} \\
     $samplesheet \\
     samplesheet.valid.csv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version | sed 's/Python //g')
-        check_samplesheet.py: \$(${ica}check_samplesheet.py --version )
+        check_samplesheet.py: ${script} --version )
         phoenix_base_container_tag: ${container_version}
         phoenix_base_container: ${container}
     END_VERSIONS

nextflow.config

@@ -41,6 +41,7 @@ params {
     // Terra and ICA specific options
     terra                       = false
     ica                         = false
+    ica_path                    = "${launchDir}/bin/"
 
     // Database paths
     //path2db                   = "${baseDir}/assets/databases" // need this for kraken2db if you place those files in the assets folder