diff --git a/tests/test_htsinfer_workflow/expected_output.md5 b/tests/test_htsinfer_workflow/expected_output.md5
index 7f585a9..22e9037 100644
--- a/tests/test_htsinfer_workflow/expected_output.md5
+++ b/tests/test_htsinfer_workflow/expected_output.md5
@@ -1,3 +1,3 @@
 1dc3f566f896b72f8f0ab8b3d60da364  results/samples_htsinfer.tsv
-642935539533503952f755dbe280fcbd  results/htsinfer_SRR1.json
-1632c04cd856a1af0abc964304d8e218  results/htsinfer_SRR2.json
+ca3f9ef26821bfa061d3b7708823ebc3  results/htsinfer_SRR1.json
+62303261f8dd73124c2a5a54cd28e572  results/htsinfer_SRR2.json
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 9f8f1ca..da8beb8 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -1,4 +1,5 @@
 """General purpose RNA-Seq analysis pipeline developed by the Zavolan Lab"""
+
 import os
 import pandas as pd
 import shutil
diff --git a/workflow/envs/cutadapt.yaml b/workflow/envs/cutadapt.yaml
index 064d302..4a42250 100644
--- a/workflow/envs/cutadapt.yaml
+++ b/workflow/envs/cutadapt.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - cutadapt=3.4
+  - cutadapt=4.6
 ...
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 2521c49..cbc2b1a 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -64,7 +64,7 @@ rule pe_remove_adapters_cutadapt:
             ),
         ),
     container:
-        "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
+        "docker://quay.io/biocontainers/cutadapt:4.6--py310h4b81fae_1"
     conda:
         os.path.join(workflow.basedir, "envs", "cutadapt.yaml")
     threads: 4
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 0f25f6c..57e13b5 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -112,7 +112,7 @@ rule remove_polya_cutadapt:
             ),
         ),
     container:
-        "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
+        "docker://quay.io/biocontainers/cutadapt:4.6--py310h4b81fae_1"
     conda:
         os.path.join(workflow.basedir, "envs", "cutadapt.yaml")
     threads: 4