From cf71148b952e8f6ed087e56a413c44c61b3c4768 Mon Sep 17 00:00:00 2001
From: Stephen Fleming <sjfleming@users.noreply.github.com>
Date: Tue, 31 Oct 2023 10:46:16 -0400
Subject: [PATCH] Bug fix for WDL using MTX input (#246)

---
 wdl/cellbender_remove_background.wdl | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/wdl/cellbender_remove_background.wdl b/wdl/cellbender_remove_background.wdl
index 6f97463..f7507ec 100644
--- a/wdl/cellbender_remove_background.wdl
+++ b/wdl/cellbender_remove_background.wdl
@@ -125,8 +125,15 @@ task run_cellbender_remove_background_gpu {
             [ -f $dir/$name ] || mv ~{genes_file} $dir/$name
         fi
 
+        # use the directory as the input in the case of an MTX file
+        if [[ "~{input_file_unfiltered}" == *.mtx* ]]; then
+            input=$(dirname ~{input_file_unfiltered})
+        else
+            input=~{input_file_unfiltered}
+        fi
+
         cellbender remove-background \
-            --input "~{input_file_unfiltered}" \
+            --input $input \
             --output "~{sample_name}_out.h5" \
             --cuda \
             ~{"--checkpoint " + checkpoint_file} \