From 6ca2f2f0272397ede2f10aba3e1d77b9b9f92c90 Mon Sep 17 00:00:00 2001
From: Natalia Garcia <natalia.garcia@nanoporetech.com>
Date: Tue, 26 May 2026 18:42:11 +0000
Subject: [PATCH] Tidy up schema validation [CW-7278]

---
 main.nf              | 71 --------------------------------------------
 nextflow_schema.json |  7 ++++-
 2 files changed, 6 insertions(+), 72 deletions(-)

diff --git a/main.nf b/main.nf
index 8d0ebd9..ea3ab07 100644
--- a/main.nf
+++ b/main.nf
@@ -90,55 +90,6 @@ process publishResults {
     """
 }
 
-def coerceBooleanParam(value) {
-    if (value == null || value instanceof Boolean) {
-        return value
-    }
-    if (value instanceof CharSequence) {
-        switch (value.toString().trim().toLowerCase()) {
-            case "true":
-            case "1":
-            case "yes":
-                return true
-            case "false":
-            case "0":
-            case "no":
-                return false
-        }
-    }
-    return value
-}
-
-
-[
-    "help",
-    "version",
-    "igv",
-    "direct_rna",
-    "de_analysis",
-    "analyse_unclassified",
-    "analyse_fail",
-    "skip_sqanti",
-    "sqanti_skip_orf",
-    "disable_ping",
-    "monochrome_logs",
-    "validate_params",
-    "show_hidden_params",
-].each { name ->
-    params[name] = coerceBooleanParam(params[name])
-}
-
-[
-    "keep_unaligned",
-    "return_fastq",
-    "per_read_stats",
-    "allow_multiple_basecall_models",
-].each { name ->
-    if (params.wf?.containsKey(name)) {
-        params.wf[name] = coerceBooleanParam(params.wf[name])
-    }
-}
-
 
 workflow pipeline {
     take:
@@ -244,28 +195,6 @@ WorkflowMain.initialise(workflow, params, log)
 workflow {
     Pinguscript.ping_start(nextflow, workflow, params)
 
-    if (params.containsKey("ref_transcriptome")) {
-        throw new Exception("--ref_transcriptome has been removed. Use --transcriptome_mode fixed_annotation with --ref_genome and --ref_annotation.")
-    }
-    if (params.containsKey("transcriptome_source")) {
-        throw new Exception("--transcriptome_source has been removed. Use --transcriptome_mode with either discover or fixed_annotation.")
-    }
-
-    if (!!params.fastq == !!params.bam) {
-        throw new Exception("Provide exactly one of --fastq or --bam.")
-    }
-    if (!params.ref_genome) {
-        throw new Exception("Provide --ref_genome.") //todo isnt this enforced in the schema?
-    }
-    if (!params.ref_annotation) {
-        throw new Exception("Provide --ref_annotation.")
-    }
-    if (!(params.transcriptome_mode in ["discover", "fixed_annotation"])) {
-        throw new Exception("--transcriptome_mode must be one of: discover, fixed_annotation.")
-    }
-    if (params.de_analysis && !params.sample_sheet) {
-        throw new Exception("Provide --sample_sheet when running with --de_analysis.")
-    }
 
     sample_sheet = params.sample_sheet ? file(params.sample_sheet, type: "file") : OPTIONAL_FILE
     ref_annotation = file(params.ref_annotation, type: "file")
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 5cf3de9..641d0ac 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -148,7 +148,12 @@
           "description": "Baseline group for the main comparison column.",
           "help_text": "If omitted, the workflow will use control when that level exists."
         }
-      }
+      },
+      "dependencies": {
+        "de_analysis": [
+            "sample_sheet"
+        ]
+    }
     },
     "output_options": {
       "title": "Output Options",