From 63d9d14f17bd2c6432a73db62504105f6737c6ad Mon Sep 17 00:00:00 2001
From: Chris Wright <chris.wright@nanoporetech.com>
Date: Tue, 5 May 2026 18:42:18 +0100
Subject: [PATCH] Fix DE validation gating and per-sample NDR

---
 subworkflows/differential_expression.nf | 5 +++--
 subworkflows/transcriptome.nf           | 2 ++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/subworkflows/differential_expression.nf b/subworkflows/differential_expression.nf
index 3caedd4..aafeada 100644
--- a/subworkflows/differential_expression.nf
+++ b/subworkflows/differential_expression.nf
@@ -31,6 +31,7 @@ process runDifferentialAnalysis {
         path transcript_rds
         path gene_rds
         path sample_sheet
+        path validation_token
     output:
         path "de_analysis", emit: dir
     script:
@@ -55,8 +56,8 @@ workflow differential_expression {
         gene_rds
         sample_sheet
     main:
-        checkExperimentDesign(sample_sheet)
-        results = runDifferentialAnalysis(transcript_rds, gene_rds, sample_sheet)
+        validated = checkExperimentDesign(sample_sheet)
+        results = runDifferentialAnalysis(transcript_rds, gene_rds, sample_sheet, validated.ok)
     emit:
         dir = results.dir
 }
diff --git a/subworkflows/transcriptome.nf b/subworkflows/transcriptome.nf
index 908329e..2ca14bd 100644
--- a/subworkflows/transcriptome.nf
+++ b/subworkflows/transcriptome.nf
@@ -209,6 +209,7 @@ process runPerSampleBambu {
         tuple val(meta), path("${meta.alias}/bambu_genes.rds"), emit: gene_rds
         tuple val(meta), path("${meta.alias}/transcript_metadata.tsv"), emit: transcript_metadata
     script:
+        String ndr_arg = params.ndr != null ? "--ndr ${params.ndr}" : ""
     """
     supeRglue bambu \
         --bam_path "${bam}" \
@@ -217,6 +218,7 @@ process runPerSampleBambu {
         --genome "${reference}" \
         --transcriptome_mode "${params.transcriptome_mode}" \
         --threads ${task.cpus} \
+        ${ndr_arg} \
         --out_dir "${meta.alias}"
     """
 }