Making help message and code more explicit that passing in a whitelis…

…t as a parameter overrides the default whitelist used by the pipeline

nextflow_schema.json

@@ -140,13 +140,13 @@
             "properties": {
                 "whitelist": {
                     "type": "string",
-                    "description": "The file containing a list of barcodes.",
+                    "description": "User-provided file containing a list of cellular barcodes. Using this parameter will override the default whitelists provided by the pipeline and use the user-provided one instead.",
                     "format": "file-path",
                     "fa_icon": "far fa-file-alt"
                 },
                 "barcode_format": {
                     "type": "string",
-                    "description": "Specify the format for the barcode+umi",
+                    "description": "Specify the format for the barcode+umi. This parameter also defines a default barcode whitelist for the pipeline to use for barcode calling, this can be overidden with the 'whitelist' parameter.",
                     "enum": ["10X_3v3", "10X_5v2"],
                     "fa_icon": "fas fa-barcode"
                 }

workflows/scnanoseq.nf

@@ -4,18 +4,17 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-
-if (params.barcode_format.equals("10X_3v3")) {
-    blaze_whitelist = file("$baseDir/assets/whitelist/3M-february-2018.zip")
-}
-else{
-    blaze_whitelist = file("$baseDir/assets/whitelist/737K-august-2016.txt.zip")
-}
-
 if (params.whitelist) {
     blaze_whitelist = params.whitelist
 }
-
+else {
+    if (params.barcode_format.equals("10X_3v3")) {
+        blaze_whitelist = file("$baseDir/assets/whitelist/3M-february-2018.zip")
+    }
+    else if (params.barcode_format.equals("10X_5v2")) {
+        blaze_whitelist = file("$baseDir/assets/whitelist/737K-august-2016.txt.zip")
+    }
+}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -121,6 +120,8 @@ workflow SCNANOSEQ {
     ch_versions = Channel.empty()
     ch_multiqc_report = Channel.empty()
 
+    Channel.of(blaze_whitelist).view()
+
     //
     // SUBWORKFLOW: Read in samplesheet, validate and stage input files
     //