diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py
index 4bfb9f4f..76878969 100644
--- a/modules/nf-core/cellranger/count/templates/cellranger_count.py
+++ b/modules/nf-core/cellranger/count/templates/cellranger_count.py
@@ -31,14 +31,25 @@ def chunk_iter(seq, size):
 fastq_all = Path("./fastq_all")
 fastq_all.mkdir(exist_ok=True)
 
+# FIXME: Generalize this filename pattern once we better understand it
+"""
+Old file name matching from NF-core
 # Match R1 in the filename, but only if it is followed by a non-digit or non-character
 # match "file_R1.fastq.gz", "file.R1_000.fastq.gz", etc. but
 # do not match "SRR12345", "file_INFIXR12", etc
-filename_pattern = r"([^a-zA-Z0-9])R1([^a-zA-Z0-9])"
+# filename_pattern = r"([^a-zA-Z0-9])R1([^a-zA-Z0-9])"
+"""
+# FIXME: This is working locally but not on AWS Batch
+# filename_pattern = r"(.+)_1"
+# print(filename_pattern)
 
 for i, (r1, r2) in enumerate(chunk_iter(fastqs, 2)):
     # double escapes are required because nextflow processes this python 'template'
-    if re.sub(filename_pattern, r"\\1R2\\2", r1.name) != r2.name:
+    # FIXME: Generalize this pattern switching function once we standardize the filename pattern
+    # if re.sub(filename_pattern, r"\\1R2\\2", r1.name) != r2.name:
+    # FIXME: This is working locally but not on AWS Batch
+    # if re.sub(filename_pattern, r"\1_2", r1.name) != r2.name:
+    if r1.name.replace("_1", "_2") != r2.name:
         raise AssertionError(
             dedent(
                 f"""\
@@ -55,11 +66,13 @@ def chunk_iter(seq, size):
     r1.rename(fastq_all / f"{sample_id}_S1_L{i:03d}_R1_001.fastq.gz")
     r2.rename(fastq_all / f"{sample_id}_S1_L{i:03d}_R2_001.fastq.gz")
 
+# FIXME: Add toggle for introns based on sc vs snRNA
 run(
     # fmt: off
     [
         "cellranger", "count",
         "--id", "${prefix}",
+        '--include-introns', 'false',
         "--fastqs", str(fastq_all),
         "--transcriptome", "${reference.name}",
         "--localcores", "${task.cpus}",