add --collapse_within option

huqiwen0313 · Dec 8, 2021 · 64b1a5c · 64b1a5c
1 parent 052fb02
commit 64b1a5c
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/rules/sinto_atac.smk b/rules/sinto_atac.smk
@@ -8,5 +8,5 @@ rule run_sinto_5:
     log:
         "tmp/logs/run_sinto_5.{sample}.log"
     run:
-        shell('sinto fragments -b {input.bam} -f {output.out1} --barcode_regex "[^:]*" 2> {log}')
+        shell('sinto fragments -b {input.bam} -f {output.out1} --barcode_regex "[^:]*" --collapse_within 2> {log}')
         shell('sort -k 1,2 -k2,2n {output.out1} > {output.out2}')