add option to ignore cli params

jimmyliu1326 · Apr 19, 2024 · 3706973 · 3706973
1 parent 364c95d
commit 3706973
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Showing 5 changed files with 16 additions and 8 deletions.
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
@@ -122,12 +122,12 @@ class NfcoreSchema {
                 has_error = true
             }
             // unexpected params
-            //def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
+            def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
             def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }
             def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
             def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase))
-            //if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
-            if (!expectedParams.contains(specifiedParam) && !isCamelCaseBug) {
+            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
+            // if (!expectedParams.contains(specifiedParam) && !isCamelCaseBug) {
                 // Temporarily remove camelCase/camel-case params #1035
                 def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}
                 if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){
@@ -142,7 +142,7 @@ class NfcoreSchema {
         JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream))
 
         // Remove anything that's in params.schema_ignore_params
-        // raw_schema = removeIgnoredParams(raw_schema, params)
+        raw_schema = removeIgnoredParams(raw_schema, params)
 
         Schema schema = SchemaLoader.load(raw_schema)
 

diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
@@ -250,7 +250,7 @@ class NfcoreTemplate {
             ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
             ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
                                                     ${colors.green}`._,._,\'${colors.reset}
-            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+            ${colors.purple}  ${workflow.manifest.name} ${workflow.manifest.version}${colors.reset}
             ${dashedLine(monochrome_logs)}
             """.stripIndent()
         )

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -55,7 +55,7 @@ class WorkflowMain {
 
         // Print pipeline version if --version is invoked
         if (params.version) {
-            log.info "${workflow.manifest.name} v${workflow.manifest.version}"
+            log.info "${workflow.manifest.name} ${workflow.manifest.version}"
             System.exit(0)
         }
 

diff --git a/nextflow.config b/nextflow.config
@@ -47,6 +47,9 @@ params {
 
     // msa options
     run_msa = false
+
+    // ignore params
+    schema_ignore_params = 'client_fields'
 }
 
 process {

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -11,9 +11,9 @@
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
             "required": [
+                "input",
                 "reference",
-                "primers",
-                "input"
+                "primers"
             ],
             "properties": {
                 "input": {
@@ -164,6 +164,11 @@
                     "type": "string",
                     "description": "Slurm account name (required for -profile slurm)"
                 },
+                "schema_ignore_params": {
+                    "type": "string",
+                    "default": "client_fields",
+                    "description": "Parameters to ignore during schema validation. Multiple values can be supplied using comma as the delimiter"
+                },
                 "help": {
                     "type": "boolean",
                     "description": "Display help text.",