fix aligner for multiqc

maxplanck-ie · Apr 9, 2024 · 209c2bf · 209c2bf
1 parent 6e93d28
commit 209c2bf
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/snakePipes/workflows/mRNA-seq/mRNA-seq b/snakePipes/workflows/mRNA-seq/mRNA-seq
@@ -175,7 +175,9 @@ def main():
     if "allelic-counting" in modeTemp and not args.fromBAM:
         warnings.warn("--fromBAM is required with allelic-counting mode. Setting to True.")
         args.fromBAM = True
-        args.aligner = "EXTERNAL_BAM"
+    if "allelic-counting" in modeTemp:
+        args.bamExt = ".sorted.bam"
+        args.aligner = "allelic_bams"
     if args.rMats and not args.sampleSheet:
         sys.exit("--rMats flag requires a sampleSheet (specified with --sampleSheet).\n")
     if "three_prime_seq" in mode: