diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5effdca5..5f577ee7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- Fixed some Nextflow run-commands in the docs [#490](https://github.com/nf-core/rnafusion/pull/490)
+
 ### Removed
 
 ## v3.0.2 - [2024-04-10]
diff --git a/README.md b/README.md
index f34ee57e..4324f210 100644
--- a/README.md
+++ b/README.md
@@ -76,8 +76,7 @@ First, build the references:
 
 ```bash
 nextflow run nf-core/rnafusion \
-   -profile <docker/singularity/.../institute> \
-   -profile test \
+   -profile test,<docker/singularity/.../institute> \
    --outdir <OUTDIR>\
    --build_references \
    -stub
@@ -87,8 +86,7 @@ Then perform the analysis:
 
 ```bash
 nextflow run nf-core/rnafusion \
-   -profile <docker/singularity/.../institute> \
-   -profile test \
+   -profile test,<docker/singularity/.../institute> \
    --outdir <OUTDIR>\
    -stub
 ```
diff --git a/docs/usage.md b/docs/usage.md
index 6ed11470..80ff457c 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -31,6 +31,7 @@ The rnafusion pipeline needs references for the fusion detection tools, so downl
 
 ```bash
 nextflow run nf-core/rnafusion \
+  -profile <docker/singularity/.../institute> \
   --build_references --all \
   --cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
   --genomes_base <PATH/TO/REFERENCES> \
@@ -41,6 +42,7 @@ References for each tools can also be downloaded separately with:
 
 ```bash
 nextflow run nf-core/rnafusion \
+  -profile <docker/singularity/.../institute> \
   --build_references --<tool1> --<tool2> ... \
   --cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
   --genomes_base <PATH/TO/REFERENCES> \
@@ -59,6 +61,7 @@ Use credentials from QIAGEN and add `--qiagen`
 
 ```bash
 nextflow run nf-core/rnafusion \
+  -profile <docker/singularity/.../institute> \
   --build_references --<tool1> --<tool2> ... \
   --cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
   --genomes_base <PATH/TO/REFERENCES> \
@@ -75,6 +78,7 @@ If process `FUSIONREPORT_DOWNLOAD` times out, it could be due to network restric
 
 ```bash
 nextflow run nf-core/rnafusion  \
+  -profile <docker/singularity/.../institute> \
   --build_references \
   --cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
   --fusionreport \
@@ -134,6 +138,7 @@ The pipeline can either be run using all fusion detection tools or specifying in
 
 ```bash
 nextflow run nf-core/rnafusion \
+  -profile <docker/singularity/.../institute> \
   --all \
   --input <SAMPLE_SHEET.CSV> \
   --genomes_base <PATH/TO/REFERENCES> \
@@ -144,6 +149,7 @@ To run only a specific detection tool use: `--tool`:
 
 ```bash
 nextflow run nf-core/rnafusion \
+  -profile <docker/singularity/.../institute> \
   --<tool1> --<tool2> ... \
   --input <SAMPLE_SHEET.CSV> \
   --genomes_base <PATH/TO/REFERENCES> \
@@ -200,6 +206,7 @@ When the flag `--fastp_trim` is used, `fastp` is used to provide all tools with
 
 ```bash
 nextflow run nf-core/rnafusion \
+-profile <docker/singularity/.../institute> \
 --<tool1> --<tool2> ... \
 --input <SAMPLE_SHEET.CSV> \
 --genomes_base <PATH/TO/REFERENCES> \
@@ -213,6 +220,7 @@ nextflow run nf-core/rnafusion \
 
 ```bash
 nextflow run nf-core/rnafusion \
+  -profile <docker/singularity/.../institute> \
   --<tool1> --<tool2> ... \
   --input <SAMPLE_SHEET.CSV> \
   --genomes_base <PATH/TO/REFERENCES> \
@@ -226,6 +234,7 @@ nextflow run nf-core/rnafusion \
 
 ```bash
 nextflow run nf-core/rnafusion \
+  -profile <docker/singularity/.../institute> \
   --<tool1> --<tool2> ... \
   --input <SAMPLE_SHEET.CSV> \
   --genomes_base <PATH/TO/REFERENCES> \
@@ -246,6 +255,7 @@ FusionInspector can be run as a standalone with:
 
 ```bash
 nextflow run nf-core/rnafusion \
+-profile <docker/singularity/.../institute> \
 --fusioninspector_only \
 --fusioninspector_fusions <PATH_TO_CUSTOM_FUSION_FILE> \
 --input <SAMPLE_SHEET.CSV> \
@@ -263,6 +273,7 @@ GENE3--GENE4
 
 ```bash
 nextflow run nf-core/rnafusion \
+-profile <docker/singularity/.../institute> \
 --skip_qc \
 --all OR <--tool>
 --input <SAMPLE_SHEET.CSV> \
@@ -276,6 +287,7 @@ This will skip all QC-related processes (picard metrics collection)
 
 ```bash
 nextflow run nf-core/rnafusion \
+-profile <docker/singularity/.../institute> \
 --skip_vis \
 --all OR <--tool>
 --input <SAMPLE_SHEET.CSV> \