From 2491edf32d3d8050addb9b46173bc5f03c33cd7b Mon Sep 17 00:00:00 2001
From: Erik Fasterius <erik.fasterius@outlook.com>
Date: Tue, 17 Dec 2024 09:07:08 +0100
Subject: [PATCH] Add functionality for `--unknown-slide` option

Add functionality to be able to use the `--unknown-slide` option of
Space Ranger Count, specified using the `slide` column in the input
samplesheet.
---
 modules/nf-core/spaceranger/count/main.nf | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf
index f33d82fcc7e..efbb1b9c734 100644
--- a/modules/nf-core/spaceranger/count/main.nf
+++ b/modules/nf-core/spaceranger/count/main.nf
@@ -31,17 +31,23 @@ process SPACERANGER_COUNT {
     def cytaimage = cytaimage ? "--cytaimage=\"${cytaimage}\"" : ""
     def darkimage = darkimage ? "--darkimage=\"${darkimage}\"" : ""
     def colorizedimage = colorizedimage ? "--colorizedimage=\"${colorizedimage}\"" : ""
+    def slide = meta.slide ? meta.slide : ""
+    def area = meta.area ? meta.area : ""
+    if (slide.matches("visium-(.*)") && area == "" && slidefile == "") {
+        slide_and_area = "--unknown-slide=\"${slide}\""
+    } else {
+        slide_and_area = "--slide=\"${slide}\" --area=\"${area}\""
+    }
     """
     spaceranger count \\
         --id="${prefix}" \\
         --sample="${meta.id}" \\
         --fastqs=. \\
-        --slide="${meta.slide}" \\
-        --area="${meta.area}" \\
         --transcriptome="${reference}" \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
         $image $cytaimage $darkimage $colorizedimage \\
+        $slide_and_area \\
         $probeset \\
         $alignment \\
         $slidefile \\