Fixed test issues

Plant-Food-Research-Open · Oct 15, 2024 · 67ef824 · 67ef824
1 parent ed795d6
commit 67ef824
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Showing 2 changed files with 12 additions and 6 deletions.
diff --git a/main.nf b/main.nf
@@ -88,7 +88,10 @@ workflow {
         params.monochrome_logs,
         args,
         params.outdir,
-        params.input
+        params.input,
+        params.rna_evidence,
+        params.liftoff_annotations,
+        params.orthofinder_annotations
     )
 
     //

diff --git a/subworkflows/local/utils_nfcore_genepal_pipeline/main.nf b/subworkflows/local/utils_nfcore_genepal_pipeline/main.nf
@@ -26,11 +26,14 @@ include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipelin
 workflow PIPELINE_INITIALISATION {
 
     take:
-    version           // boolean: Display version and exit
-    monochrome_logs   // boolean: Do not use coloured log outputs
-    nextflow_cli_args //   array: List of positional nextflow CLI args
-    outdir            //  string: The output directory where the results will be saved
-    input             //  string: Path to input samplesheet
+    version                 // boolean: Display version and exit
+    monochrome_logs         // boolean: Do not use coloured log outputs
+    nextflow_cli_args       //   array: List of positional nextflow CLI args
+    outdir                  //  string: The output directory where the results will be saved
+    input                   //  string: Path to input assemblysheet
+    rna_evidence            //  string: Path to rna samplesheet
+    liftoff_annotations     //  string: Path to liftoff annotations sheet
+    orthofinder_annotations //  string: Path to orthofinder annotations sheet
 
     main: