From 7582f30cecd7423fdb8a45d7b1afd5ef1579d615 Mon Sep 17 00:00:00 2001
From: eolaniru <149598276+eolaniru@users.noreply.github.com>
Date: Tue, 13 Aug 2024 12:40:17 +0100
Subject: [PATCH] error message when feature barcoding ref is not specified

---
 subworkflows/local/align_cellrangermulti.nf | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf
index f853c001..977bf478 100644
--- a/subworkflows/local/align_cellrangermulti.nf
+++ b/subworkflows/local/align_cellrangermulti.nf
@@ -43,7 +43,11 @@ workflow CELLRANGER_MULTI_ALIGN {
                 vdj: meta.feature_type == "vdj"
                     return [ meta, fastq ]
                 ab: meta.feature_type == "ab"
-                    return [ meta, fastq ]
+                    if (params.fb_reference){
+                        return [ meta, fastq ]
+                    } else {
+                        error ("Antibody reference was not specified. Please provide a reference file for feature barcoding (e.g. antibody measurements).\nPlease refer to https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-feature-ref-csv for more details.")
+                    }
                 beam: meta.feature_type == "beam"
                     return [ meta, fastq ]
                 crispr: meta.feature_type == "crispr"