diff --git a/bio/deeptools/plotfingerprint/test/Snakefile b/bio/deeptools/plotfingerprint/test/Snakefile
index d3cca05ce1..888da5cec4 100644
--- a/bio/deeptools/plotfingerprint/test/Snakefile
+++ b/bio/deeptools/plotfingerprint/test/Snakefile
@@ -2,7 +2,7 @@ rule plot_fingerprint:
     input:
         bam_files=expand("samples/{sample}.bam", sample=["a", "b"]),
         bam_idx=expand("samples/{sample}.bam.bai", sample=["a", "b"]),
-        jsd_sample="samples/b.bam" # optional, requires qc_metrics output
+        jsd_sample="samples/b.bam",  # optional, requires qc_metrics output
     output:
         # Please note that --plotFile and --outRawCounts are exclusively defined via output files.
         # Usable output variables, their extensions and which option they implicitly call are listed here:
@@ -10,13 +10,12 @@ rule plot_fingerprint:
         fingerprint="plot_fingerprint/plot_fingerprint.png",  # required
         # optional output
         counts="plot_fingerprint/raw_counts.tab",
-        qc_metrics="plot_fingerprint/qc_metrics.txt"
+        qc_metrics="plot_fingerprint/qc_metrics.txt",
     log:
-        "logs/deeptools/plot_fingerprint.log"
+        "logs/deeptools/plot_fingerprint.log",
     params:
         # optional parameters
-        "--numberOfSamples 200 "
-    threads:
-        8
+        extra="--numberOfSamples 200",
+    threads: 8
     wrapper:
         "master/bio/deeptools/plotfingerprint"
diff --git a/bio/deeptools/plotfingerprint/wrapper.py b/bio/deeptools/plotfingerprint/wrapper.py
index b1059f5390..5cb6668699 100644
--- a/bio/deeptools/plotfingerprint/wrapper.py
+++ b/bio/deeptools/plotfingerprint/wrapper.py
@@ -1,12 +1,14 @@
 __author__ = "Antonie Vietor"
-__copyright__ = "Copyright 2020, Antonie Vietor"
+__copyright__ = "Copyright 2024, Antonie Vietor, Lance Parsons"
 __email__ = "antonie.v@gmx.de"
 __license__ = "MIT"
 
-from snakemake.shell import shell
 import re
 
+from snakemake.shell import shell
+
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
 
 jsd_sample = snakemake.input.get("jsd_sample")
 out_counts = snakemake.output.get("counts")
@@ -30,16 +32,5 @@
     "{optional_output} "
     "--numberOfProcessors {snakemake.threads} "
     "{jsd} "
-    "{snakemake.params}) {log}"
+    "{extra}) {log}"
 )
-# ToDo: remove the 'NA' string replacement when fixed in deepTools, see:
-# https://github.com/deeptools/deepTools/pull/999
-regex_passes = 2
-
-with open(out_metrics, "rt") as f:
-    metrics = f.read()
-    for i in range(regex_passes):
-        metrics = re.sub("\tNA(\t|\n)", "\tnan\\1", metrics)
-
-with open(out_metrics, "wt") as f:
-    f.write(metrics)
diff --git a/bio/deeptools/plotheatmap/test/Snakefile b/bio/deeptools/plotheatmap/test/Snakefile
index facc208a6d..812ef6b214 100644
--- a/bio/deeptools/plotheatmap/test/Snakefile
+++ b/bio/deeptools/plotheatmap/test/Snakefile
@@ -14,6 +14,6 @@ rule plot_heatmap:
         "logs/deeptools/heatmap.log"
     params:
         # optional parameters
-        "--plotType=fill "
+        extra="--plotType=fill "
     wrapper:
         "master/bio/deeptools/plotheatmap"
diff --git a/bio/deeptools/plotheatmap/wrapper.py b/bio/deeptools/plotheatmap/wrapper.py
index a963064387..eae24a605e 100644
--- a/bio/deeptools/plotheatmap/wrapper.py
+++ b/bio/deeptools/plotheatmap/wrapper.py
@@ -6,6 +6,7 @@
 from snakemake.shell import shell
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
 
 out_region = snakemake.output.get("regions")
 out_matrix = snakemake.output.get("heatmap_matrix")
@@ -27,5 +28,5 @@
     "-m {snakemake.input[0]} "
     "-o {snakemake.output.heatmap_img} "
     "{optional_output} "
-    "{snakemake.params}) {log}"
+    "{extra}) {log}"
 )
diff --git a/bio/deeptools/plotprofile/test/Snakefile b/bio/deeptools/plotprofile/test/Snakefile
index 8156ea47e6..b1e77bf60a 100644
--- a/bio/deeptools/plotprofile/test/Snakefile
+++ b/bio/deeptools/plotprofile/test/Snakefile
@@ -15,9 +15,6 @@ rule plot_profile:
         "logs/deeptools/plot_profile.log"
     params:
         # optional parameters
-        "--plotType=fill "
-        "--perGroup "
-        "--colors red yellow blue "
-        "--dpi 150 "
+        extra="--plotType=fill --perGroup --colors red yellow blue --dpi 150"
     wrapper:
         "master/bio/deeptools/plotprofile"
diff --git a/bio/deeptools/plotprofile/wrapper.py b/bio/deeptools/plotprofile/wrapper.py
index 9fcc8b875d..7d6c98a3dc 100644
--- a/bio/deeptools/plotprofile/wrapper.py
+++ b/bio/deeptools/plotprofile/wrapper.py
@@ -6,6 +6,7 @@
 from snakemake.shell import shell
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
 
 out_region = snakemake.output.get("regions")
 out_data = snakemake.output.get("data")
@@ -25,5 +26,5 @@
     "-m {snakemake.input[0]} "
     "-o {snakemake.output.plot_img} "
     "{optional_output} "
-    "{snakemake.params}) {log}"
+    "{extra}) {log}"
 )