Fixes to template

nf-core · Oct 8, 2024 · d1eb4a9 · d1eb4a9
1 parent 01a1b1f
commit d1eb4a9
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Showing 3 changed files with 8 additions and 7 deletions.
diff --git a/main.nf b/main.nf
@@ -70,6 +70,7 @@ workflow {
     //
     PIPELINE_INITIALISATION (
         params.version,
+        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -479,22 +479,22 @@
             "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/umi_options"
+            "$ref": "#/$defs/umi_options"
         },
         {
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/trimming_options"
+            "$ref": "#/$defs/trimming_options"
         },
         {
-            "$ref": "#/definitions/contamination_filtering"
+            "$ref": "#/$defs/contamination_filtering"
         },
         {
-            "$ref": "#/definitions/skipping_pipeline_steps"
+            "$ref": "#/$defs/skipping_pipeline_steps"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
             "$ref": "#/$defs/generic_options"

diff --git a/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf
@@ -84,7 +84,7 @@ workflow PIPELINE_INITIALISATION {
     // Create channel from input file provided through params.input
     //
 
-    Channel
+    ch_samplesheet = Channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->