add markDuplicate in workflow #37

workflow/rules/mark_duplicates.rules

@@ -28,16 +28,16 @@ rule mark_duplicates:
     output:
         bam = mark_duplicates_output,
         metrics = mark_duplicates_metrics
-    singularity:
-        "rnaflow.img"
-    log:
-        out = mark_duplicates_log_std,
-        err = mark_duplicates_log_err
     params:
         remove_dup = config["mark_duplicates"]["remove"],
         tmpdir = mark_duplicates_tmpdir
     threads:
         int(config["mark_duplicates"]["threads"])
+    log:
+        out = mark_duplicates_log_std,
+        err = mark_duplicates_log_err
+    singularity:
+        "rnaflow.img"
     envmodules:
         "samtools",
         "graalvm/ce-java8-20.0.0",