diff --git a/sequana_pipelines/mapper/config.yaml b/sequana_pipelines/mapper/config.yaml
index ac299bc..8314851 100644
--- a/sequana_pipelines/mapper/config.yaml
+++ b/sequana_pipelines/mapper/config.yaml
@@ -6,8 +6,6 @@
 # If input_directory provided, use it otherwise if input_pattern provided,
 # use it, otherwise use input_samples.
 # ============================================================================
-sequana_wrappers: v24.8.29
-
 input_directory:
 input_readtag: _R[12]_
 input_pattern: '*fastq.gz'
diff --git a/sequana_pipelines/mapper/main.py b/sequana_pipelines/mapper/main.py
index 3e6e31b..adce2d8 100755
--- a/sequana_pipelines/mapper/main.py
+++ b/sequana_pipelines/mapper/main.py
@@ -124,11 +124,11 @@ def main(**options):
 
     # seems to be a hardcoded values in bwa according to the documentation
     if N >= 2000000000:
-        cfg["bwa"]["index_algorithm"] = "bwtsw"
-        cfg["bwa_split"]["index_algorithm"] = "bwtsw"
+        cfg.bwa.index_algorithm = "bwtsw"
+        cfg.bwa_split.index_algorithm = "bwtsw"
     else:
-        cfg["bwa"]["index_algorithm"] = "is"
-        cfg["bwa_split"]["index_algorithm"] = "is"
+        cfg.bwa.index_algorithm = "is"
+        cfg.bwa_split.index_algorithm = "is"
 
     # finalise the command and save it; copy the snakemake. update the config
     # file and save it.
diff --git a/sequana_pipelines/mapper/mapper.rules b/sequana_pipelines/mapper/mapper.rules
index b207997..cf9d2ef 100644
--- a/sequana_pipelines/mapper/mapper.rules
+++ b/sequana_pipelines/mapper/mapper.rules
@@ -370,18 +370,15 @@ if config["general"]["create_bigwig"]:
 
 # ========================================================== multiqc
 
-multiqc_params_options = config['multiqc']['options']
-if manager.config.multiqc.config_file:
-    multiqc_params_options += f" -c {manager.config.multiqc.config_file}"
-
 rule multiqc:
     input:
         get_multiqc_inputs()
     output:
        "multiqc/multiqc_report.html"
     params:
-        options=multiqc_params_options,
+        options=config['multiqc']['options'],
         input_directory=config['multiqc']['input_directory'],
+        config_file=config['multiqc']['config_file'],
         modules=config['multiqc']['modules']
     log:
         "multiqc/multiqc.log"
@@ -400,8 +397,8 @@ rule rulegraph:
     params:
         mapper = {"multiqc": "../multiqc/multiqc_report.html"},
         configname = "config.yaml"
-    wrapper:
-        f"{manager.wrappers}/wrappers/rulegraph"
+    run:
+        manager.get_run("rulegraph/run", "v1")(input, output, params)
 
 
 rule dot2svg:
@@ -412,7 +409,7 @@ rule dot2svg:
     container:
         config['apptainers']['graphviz']
     shell:
-        """dot -Tsvg {input} -o {output}"""
+        manager.get_shell("graphviz/dot2svg", "v1")
 
 
 # Those rules takes a couple of seconds so no need for a cluster
diff --git a/sequana_pipelines/mapper/schema.yaml b/sequana_pipelines/mapper/schema.yaml
index e83a8d1..f56cc04 100644
--- a/sequana_pipelines/mapper/schema.yaml
+++ b/sequana_pipelines/mapper/schema.yaml
@@ -3,9 +3,6 @@
 
 type: map
 mapping:
-    "sequana_wrappers":
-        type: str
-        required: true
     "input_directory":
         type: str
         required: True