diff --git a/bio/qualimap/bamqc/meta.yaml b/bio/qualimap/bamqc/meta.yaml
index d3f77cf2cdd..70ce4cd58a0 100644
--- a/bio/qualimap/bamqc/meta.yaml
+++ b/bio/qualimap/bamqc/meta.yaml
@@ -1,4 +1,4 @@
-name: qualimap rnaseq
+name: qualimap bamqc
 description: |
         Run qualimap bamqc to create a QC report for aligned NGS data data. It can be
         used for WGS, WES, RNA, ChIP-Seq, etc.
diff --git a/bio/qualimap/bamqc/wrapper.py b/bio/qualimap/bamqc/wrapper.py
index ebd49d19b07..6c41fcb50b1 100644
--- a/bio/qualimap/bamqc/wrapper.py
+++ b/bio/qualimap/bamqc/wrapper.py
@@ -1,4 +1,4 @@
-__author__ = "Fritjof Lammers"
+__author__ = "Fritjof Lammers, Christopher Schröder"
 __copyright__ = "Copyright 2022, Fritjof Lammers"
 __email__ = "f.lammers@dkfz.de"
 
@@ -6,12 +6,14 @@
 
 
 import os
-
 from snakemake.shell import shell
 from snakemake_wrapper_utils.java import get_java_opts
 
-java_opts = get_java_opts(snakemake)
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
+# Set JAVA options
+java_opts = get_java_opts(snakemake)
 if java_opts:
     java_opts_str = f'JAVA_OPTS="{java_opts}"'
 else:
@@ -21,11 +23,15 @@
 if os.environ.get("DISPLAY"):
     del os.environ["DISPLAY"]
 
-extra = snakemake.params.get("extra", "")
-log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+if target := snakemake.input.get("target", ""):
+    target = f"--feature-file {target}"
+
 shell(
-    "{java_opts_str} qualimap bamqc {extra} "
-    "-bam {snakemake.input.bam} "
-    "-outdir {snakemake.output} "
-    "{log}"
+    "{java_opts_str} qualimap bamqc"
+    " -nt {snakemake.threads}"
+    " -bam {snakemake.input.bam}"
+    " {target}"
+    " {extra}"
+    " -outdir {snakemake.output}"
+    " {log}"
 )