From 0b030b13f7968a8b278b70b5a8196fe0f8ad85ec Mon Sep 17 00:00:00 2001
From: Sara Sjunnebo <sara.sjunnebo@gmail.com>
Date: Mon, 7 Oct 2024 12:02:03 +0200
Subject: [PATCH] Return empty string instead of None for missing I2

---
 taca/element/Element_Runs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/taca/element/Element_Runs.py b/taca/element/Element_Runs.py
index 34cea966..6550756c 100644
--- a/taca/element/Element_Runs.py
+++ b/taca/element/Element_Runs.py
@@ -32,7 +32,7 @@ def get_mask(
 
     # Input assertions
     if not seq:
-        return None
+        return ""
     assert re.match(r"^[ACGTN]+$", seq), f"Index '{seq}' has non-ACGTN characters"
     assert mask_type in ["umi", "index"], "Mask type must be 'umi' or 'index'"
     assert prefix in [
@@ -525,7 +525,7 @@ def make_demux_manifests(
                 ]
             )
             
-            if I2Mask:
+            if I2Mask != "":
                 settings_section += f"\nI2Mask, {I2Mask}"
 
             if group["has_umi"].all():