Clarify --countReadPairs flag for paired-end fragment counting

Ekin-Kahraman · Ekin-Kahraman · commit 8fd4ab8c6765 · 2026-04-05T20:41:41.000+01:00
diff --git a/main.nf b/main.nf
@@ -170,7 +170,7 @@ process FEATURECOUNTS {
         -a ${gtf} \
         -o gene_counts.txt \
         -T 4 \
-        -p --countReadPairs \
+        -p --countReadPairs \  # count fragments, not individual reads (PE data)
         -s ${params.strandedness} \
         -t exon \
         -g gene_name \
