diff --git a/utils/nextflow/meta.yaml b/utils/nextflow/meta.yaml
index 914b3a353e3..65f34f91139 100644
--- a/utils/nextflow/meta.yaml
+++ b/utils/nextflow/meta.yaml
@@ -5,4 +5,8 @@ authors:
 notes: |
   This wrapper can e.g. be used to run `nf-core <https://nf-co.re>`_ pipelines. 
   In each of the nf-core pipeline descriptions, you will find available parameters and the output file structure (under "aws results"). 
-  The latter can be used to set the desired output files for this wrapper.
\ No newline at end of file
+  The latter can be used to set the desired output files for this wrapper.
+params:
+  launch_dir: |
+    Allows adjusting the directory from which nextflow is launched.
+    Nextflow itself does not allow doing so; it always sets launchDir (read-only) from where it was invoked.
diff --git a/utils/nextflow/test/Snakefile b/utils/nextflow/test/Snakefile
index 8b2562bb8d6..29d69866223 100644
--- a/utils/nextflow/test/Snakefile
+++ b/utils/nextflow/test/Snakefile
@@ -44,15 +44,18 @@ rule chipseq_pipeline:
         gtf="data/genome.gtf",
         # any --<argname> pipeline file arguments can be given here as <argname>=<path>
     output:
-        "results/multiqc/broadPeak/multiqc_report.html",
+        multiqc_report="results/multiqc/broadPeak/multiqc_report.html",
+        # directory from which nextflow is launched, will contain the `.nextflow` directory
+        launch_dir=directory("some_directory"),
     params:
         pipeline="nf-core/chipseq",
         revision="2.0.0",
         profile=["test", "docker"],
+        launch_dir=lambda wildcards, output: output.launch_dir,
         # The chosen pipeline expects an --outdir to be given.
         # We infer this from the output file path. Since that file path can be changed
         # e.g. in case of cloud storage, we use a lambda function to infer the outdir.
-        outdir=lambda wildcards, output: str(Path(output[0]).parents[-2]),
+        outdir=lambda wildcards, output: str(Path(output.multiqc_report).parents[-2]),
         # any --<argname> pipeline arguments can be given here as <argname>=<value>
     handover: True
     wrapper:
diff --git a/utils/nextflow/wrapper.py b/utils/nextflow/wrapper.py
index ea5c8cbde2b..23b49c74997 100644
--- a/utils/nextflow/wrapper.py
+++ b/utils/nextflow/wrapper.py
@@ -32,16 +32,18 @@
         files = ",".join(files)
     add_parameter(name, files)
 for name, value in snakemake.params.items():
-    if (
-        name != "pipeline"
-        and name != "revision"
-        and name != "profile"
-        and name != "extra"
-    ):
+    if name not in {"pipeline", "revision", "profile", "extra", "launch_dir"}:
         add_parameter(name, value)
 
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 args = " ".join(args)
 pipeline = snakemake.params.pipeline
 
+launch_dir = snakemake.params.get("launch_dir")
+if launch_dir:
+    if not os.path.isdir(launch_dir):
+        raise ValueError(f"launch_dir does not exist: {launch_dir}")
+    else:
+        os.chdir(launch_dir)
+
 shell("nextflow run {pipeline} {args} {extra} {log}")