From a3c49ef39a58b54836f2aeae74f46b70092cbd9e Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Mon, 6 Sep 2021 12:21:06 -0600
Subject: [PATCH 1/2] display enum choices on error

---
 .../pipeline-template/lib/NfcoreSchema.groovy | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/lib/NfcoreSchema.groovy b/nf_core/pipeline-template/lib/NfcoreSchema.groovy
index 8d6920dd64..07a2387a38 100755
--- a/nf_core/pipeline-template/lib/NfcoreSchema.groovy
+++ b/nf_core/pipeline-template/lib/NfcoreSchema.groovy
@@ -105,9 +105,13 @@ class NfcoreSchema {
 
         // Collect expected parameters from the schema
         def expectedParams = []
+        def enums = [:]
         for (group in schemaParams) {
             for (p in group.value['properties']) {
                 expectedParams.push(p.key)
+                if (group.value['properties'][p.key].containsKey('enum')) {
+                    enums[p.key] = group.value['properties'][p.key]['enum']
+                }
             }
         }
 
@@ -155,7 +159,7 @@ class NfcoreSchema {
             println ''
             log.error 'ERROR: Validation of pipeline parameters failed!'
             JSONObject exceptionJSON = e.toJSON()
-            printExceptions(exceptionJSON, params_json, log)
+            printExceptions(exceptionJSON, params_json, log, enums)
             println ''
             has_error = true
         }
@@ -330,7 +334,7 @@ class NfcoreSchema {
     //
     // Loop over nested exceptions and print the causingException
     //
-    private static void printExceptions(ex_json, params_json, log) {
+    private static void printExceptions(ex_json, params_json, log, enums, limit=5) {
         def causingExceptions = ex_json['causingExceptions']
         if (causingExceptions.length() == 0) {
             def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
@@ -346,7 +350,16 @@ class NfcoreSchema {
             else {
                 def param = ex_json['pointerToViolation'] - ~/^#\//
                 def param_val = params_json[param].toString()
-                log.error "* --${param}: ${ex_json['message']} (${param_val})"
+                if (enums.containsKey(param)) {
+                    def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices"
+                    if (enums[param].size() > limit) {
+                        log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )"
+                    } else {
+                        log.error "${error_msg}: ${enums[param][].join(', ')})"
+                    }
+                } else {
+                    log.error "* --${param}: ${ex_json['message']} (${param_val})"
+                }
             }
         }
         for (ex in causingExceptions) {

From 12103eb2675937b3d0c64510858f4074a56d3165 Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Mon, 6 Sep 2021 12:27:20 -0600
Subject: [PATCH 2/2] fix typo

---
 nf_core/pipeline-template/lib/NfcoreSchema.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/lib/NfcoreSchema.groovy b/nf_core/pipeline-template/lib/NfcoreSchema.groovy
index 07a2387a38..4ee0b989b5 100755
--- a/nf_core/pipeline-template/lib/NfcoreSchema.groovy
+++ b/nf_core/pipeline-template/lib/NfcoreSchema.groovy
@@ -355,7 +355,7 @@ class NfcoreSchema {
                     if (enums[param].size() > limit) {
                         log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )"
                     } else {
-                        log.error "${error_msg}: ${enums[param][].join(', ')})"
+                        log.error "${error_msg}: ${enums[param].join(', ')})"
                     }
                 } else {
                     log.error "* --${param}: ${ex_json['message']} (${param_val})"