Add more prominent warnings about using custom config to provide para…

…meters

README.md

@@ -98,6 +98,8 @@ A number of improvements were made to the pipeline recently, mainly with regard
 
 4. Start running your own analysis!
 
+   > - Parameters passed via custom config files including the `-c` Nextflow option will be ignored. Please provide pipeline parameters via the `-params-file` Nextflow option instead; see [docs](https://nf-co.re/usage/configuration?q=params#custom-configuration-files).
+
    - Typical command for Illumina shotgun analysis:
 
      ```bash

docs/usage.md

@@ -4,6 +4,10 @@
 
 > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
 
+## Pipeline parameters
+
+Parameters passed via custom config files including the `-c` Nextflow option will be ignored. Please provide pipeline parameters via the `-params-file` Nextflow option instead; see [docs](https://nf-co.re/usage/configuration?q=params#custom-configuration-files).
+
 ## Samplesheet format
 
 ### Illumina

lib/NfcoreTemplate.groovy

@@ -32,6 +32,18 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    //  Warn if using custom configs to provide pipeline parameters
+    //
+    public static void warnParamsProvidedInConfig(workflow, log) {
+        if (workflow.configFiles.size() > 1) {
+            log.warn "[$workflow.manifest.name] Multiple config files detected!\n" +
+                    "Parameters passed via custom config files including the '-c' Nextflow option will be ignored.\n" +
+                    "Please provide pipeline parameters via the '-params-file' Nextflow option instead.\n" +
+                    "Docs: https://nf-co.re/usage/configuration?q=params#custom-configuration-files\n"
+        }
+    }
+
     //
     // Generate version string
     //

lib/WorkflowMain.groovy

@@ -62,6 +62,9 @@ class WorkflowMain {
         // Print parameter summary log to screen
         log.info paramsSummaryLog(workflow, params, log)
 
+        // Warn about using custom configs to provide pipeline parameters
+        NfcoreTemplate.warnParamsProvidedInConfig(workflow, log)
+
         // Validate workflow parameters via the JSON schema
         if (params.validate_params) {
             NfcoreSchema.validateParameters(workflow, params, log)