diff --git a/test.py b/test.py
index 35aadbd6172..b4764778596 100644
--- a/test.py
+++ b/test.py
@@ -5602,7 +5602,14 @@ def test_ensembl_annotation_gtf_gz():
 def test_ensembl_regulatory_gff3_gz():
     run(
         "bio/reference/ensembl-regulation",
-        ["snakemake", "--cores", "1", "resources/regulatory_features.gff3.gz", "--use-conda", "-F"],
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "resources/regulatory_features.gff3.gz",
+            "--use-conda",
+            "-F",
+        ],
     )
 
 
@@ -5610,7 +5617,14 @@ def test_ensembl_regulatory_gff3_gz():
 def test_ensembl_regulatory_features_grch37_gff():
     run(
         "bio/reference/ensembl-regulation",
-        ["snakemake", "--cores", "1", "resources/regulatory_features.gff", "--use-conda", "-F"],
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "resources/regulatory_features.gff",
+            "--use-conda",
+            "-F",
+        ],
     )
 
 
@@ -5618,7 +5632,14 @@ def test_ensembl_regulatory_features_grch37_gff():
 def test_ensembl_regulatory_features_mouse_gff_gz():
     run(
         "bio/reference/ensembl-regulation",
-        ["snakemake", "--cores", "1", "resources/regulatory_features.mouse.gff.gz", "--use-conda", "-F"],
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "resources/regulatory_features.mouse.gff.gz",
+            "--use-conda",
+            "-F",
+        ],
     )
 
 
@@ -6710,3 +6731,101 @@ def test_emu_combine_output_split():
             "-F",
         ],
     )
+
+
+@skip_if_not_modified
+def test_quarto_simple_html():
+    run(
+        "utils/quarto",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "output/simple.html",
+            "--use-conda",
+        ],
+    )
+
+
+@skip_if_not_modified
+def test_quarto_simple_docx():
+    run(
+        "utils/quarto",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "output/simple.docx",
+            "--use-conda",
+        ],
+    )
+
+
+@skip_if_not_modified
+def test_quarto_simple_parameters():
+    run(
+        "utils/quarto",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "output/example_proj_full.html",
+            "--use-conda",
+        ],
+    )
+
+
+@skip_if_not_modified
+def test_quarto_simple_noreport():
+    run(
+        "utils/quarto",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "output/example_proj_noreport.txt",
+            "--use-conda",
+        ],
+    )
+
+
+@skip_if_not_modified
+def test_quarto_simple_extra_renv_deps():
+    run(
+        "utils/quarto",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "output/extra_datatable_renv.html",
+            "--use-conda",
+        ],
+    )
+
+
+@skip_if_not_modified
+def test_quarto_pass_resources():
+    run(
+        "utils/quarto",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "output/resources_custom.html",
+            "--use-conda",
+        ],
+    )
+
+
+@skip_if_not_modified
+def test_quarto_pass_threads():
+    run(
+        "utils/quarto",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "output/resources_threads.html",
+            "--use-conda",
+        ],
+    )
diff --git a/utils/quarto/environment.linux-64.pin.txt b/utils/quarto/environment.linux-64.pin.txt
new file mode 100644
index 00000000000..243c64641ff
--- /dev/null
+++ b/utils/quarto/environment.linux-64.pin.txt
@@ -0,0 +1,138 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080
+https://conda.anaconda.org/conda-forge/linux-64/dart-sass-1.58.3-ha770c72_1.conda#d54982a58cd9be3d00a7efe76ba6f60c
+https://conda.anaconda.org/conda-forge/linux-64/esbuild-0.19.2-ha770c72_0.conda#8fa87b764cf6143cb66e9cc3548b186a
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_17.conda#d731b543793afc0433c4fd593e693fce
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74
+https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.2.0-hdb50d1a_111.conda#43178c27fac2dcd495bd9e58e18272d9
+https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-hdb50d1a_111.conda#4ffa92ea4ba6555dee156ce3d0ae7a9b
+https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.1.11.1-ha770c72_0.conda#0e2f14aff42adf4675bcd5335d644a5f
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
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+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
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+https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e
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+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559
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+https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a
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+https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.1-hd590300_0.conda#b462a33c0be1421532f28bfe8f4a7514
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+https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h7f98852_1002.tar.bz2#06feff3d2634e3097ce2fe681474b534
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+https://conda.anaconda.org/conda-forge/noarch/r-packrat-0.9.2-r43hc72bb7e_0.conda#acc0bee43ed5a63ef521aa6995541e97
+https://conda.anaconda.org/conda-forge/linux-64/r-ps-1.7.6-r43h57805ef_0.conda#48f9e73215aa6de4545ec3ec36e5e534
+https://conda.anaconda.org/conda-forge/noarch/r-r6-2.5.1-r43hc72bb7e_2.conda#79f167972554dc6b65aa099cd85c22a1
+https://conda.anaconda.org/conda-forge/linux-64/r-rappdirs-0.3.3-r43h57805ef_2.conda#788ac4f3dcfa79520bfc9eeadf50c2eb
+https://conda.anaconda.org/conda-forge/linux-64/r-rcpp-1.0.12-r43h7df8631_0.conda#a8aac8be0868617b28f27484ea548d6c
+https://conda.anaconda.org/conda-forge/noarch/r-renv-1.0.7-r43hc72bb7e_0.conda#efa116dc4d7118a48c97f6f8f4861427
+https://conda.anaconda.org/conda-forge/linux-64/r-rlang-1.1.4-r43ha18555a_0.conda#74c4cb6644843dccabc350cba4b56ec6
+https://conda.anaconda.org/conda-forge/noarch/r-rstudioapi-0.16.0-r43hc72bb7e_0.conda#02c7b3c36e390b0c538300adab8ca3eb
+https://conda.anaconda.org/conda-forge/linux-64/r-sys-3.4.2-r43h57805ef_1.conda#ae6e4dd935d9c91064cbca07d2769d75
+https://conda.anaconda.org/conda-forge/linux-64/r-xfun-0.45-r43ha18555a_0.conda#cced29e73709a7c9b2495a4f5d695d66
+https://conda.anaconda.org/conda-forge/linux-64/r-yaml-2.3.8-r43h57805ef_0.conda#41db1ee9d0073339e681379b92e7dfb6
+https://conda.anaconda.org/conda-forge/linux-64/r-askpass-1.2.0-r43h57805ef_0.conda#ee095f1d72a1d80864816e44623ba392
+https://conda.anaconda.org/conda-forge/linux-64/r-cachem-1.1.0-r43hb1dbf0f_0.conda#d48720030e2b1d780389bafa5a9c7536
+https://conda.anaconda.org/conda-forge/linux-64/r-ellipsis-0.3.2-r43h57805ef_2.conda#10c5892991072cfa3a61489d2ac6ad66
+https://conda.anaconda.org/conda-forge/noarch/r-highr-0.11-r43hc72bb7e_0.conda#ecd3b95a01caa7bdcf63714427b5b88c
+https://conda.anaconda.org/conda-forge/linux-64/r-later-1.3.2-r43ha503ecb_0.conda#6e120827a341f21444881e84408e98a7
+https://conda.anaconda.org/conda-forge/noarch/r-lifecycle-1.0.4-r43hc72bb7e_0.conda#291d2fb68ea1b181644b40d6743ae000
+https://conda.anaconda.org/conda-forge/linux-64/r-pki-0.1_14-r43hb1dbf0f_0.conda#58c4dc882730c0d96ca09e58be0150d8
+https://conda.anaconda.org/conda-forge/linux-64/r-processx-3.8.4-r43h57805ef_0.conda#660d4e9ff8beef35dbda645484d17a25
+https://conda.anaconda.org/conda-forge/noarch/r-tinytex-0.51-r43hc72bb7e_0.conda#16653f65f1ab934e1a9bdac874f9b63b
+https://conda.anaconda.org/conda-forge/linux-64/r-htmltools-0.5.8.1-r43ha503ecb_0.conda#220b9c45f5867a42d49bde8d340e9e53
+https://conda.anaconda.org/conda-forge/noarch/r-knitr-1.47-r43hc72bb7e_0.conda#0310660d998a5933bb4545a312ed7385
+https://conda.anaconda.org/conda-forge/noarch/r-memoise-2.0.1-r43hc72bb7e_2.conda#6520452e207d8f9bab9f21492f88c48b
+https://conda.anaconda.org/conda-forge/linux-64/r-openssl-2.2.0-r43hd7d0243_0.conda#60f961514ecc3ee1fd7b1afd6ea853ab
+https://conda.anaconda.org/conda-forge/noarch/r-fontawesome-0.5.2-r43hc72bb7e_0.conda#d07f215759462959de39d7232386f1b9
+https://conda.anaconda.org/conda-forge/noarch/r-jquerylib-0.1.4-r43hc72bb7e_2.conda#49a3fad710cbccec9139b36587842f88
+https://conda.anaconda.org/conda-forge/noarch/r-rsconnect-1.3.1-r43hc72bb7e_0.conda#474409574da3aacf988008567cbf11b7
+https://conda.anaconda.org/conda-forge/linux-64/r-sass-0.4.9-r43ha503ecb_0.conda#58e32ad6d979828aa0fc3da59e1b4d78
+https://conda.anaconda.org/conda-forge/noarch/r-bslib-0.7.0-r43hc72bb7e_0.conda#6e2bfdc782284259390d09bb083142b2
+https://conda.anaconda.org/conda-forge/noarch/r-rmarkdown-2.27-r43hc72bb7e_1.conda#4b681e35650d7d10737bc0c6ed80ae9a
+https://conda.anaconda.org/conda-forge/noarch/r-quarto-1.4-r43hc72bb7e_0.conda#a86d89513116deba7cc3c6e8e72a0f61
diff --git a/utils/quarto/environment.yaml b/utils/quarto/environment.yaml
new file mode 100644
index 00000000000..dacd6737517
--- /dev/null
+++ b/utils/quarto/environment.yaml
@@ -0,0 +1,5 @@
+channels:
+    - conda-forge
+    - nodefaults
+dependencies:
+    - r-quarto=1.4
\ No newline at end of file
diff --git a/utils/quarto/meta.yaml b/utils/quarto/meta.yaml
new file mode 100644
index 00000000000..46f9634108b
--- /dev/null
+++ b/utils/quarto/meta.yaml
@@ -0,0 +1,53 @@
+name: quarto
+description: Render quarto markdown documents
+url: https://github.com/quarto-dev/quarto-r
+authors:
+  -Vito Zanotelli
+input:
+  - script: |
+      Quarto script to render (.qmd).
+      - The script must follow the following rules:
+        - If parameters are used (extra arguments in `input`, `output`, `params`)
+          they must be defined in the quarto header as params: https://quarto.org/docs/computations/parameters.html#knitr
+        - resources passed to the script must be defined in the quarto header as `resources_` followed by the resource name.
+          Eg `resources_mem` entry in the quarto header would cause the `sm.resources.mem` passed to the quarto script.
+          Threads will be passed if a parameter `resources_threads` is defined in the quarto header.
+        - All dependencies used in the script must either be:
+          - installed in the `renv` declared as `input.renv` (see `input.renv` documentation)
+          - installed in the conda environment used to run this wrapper. If this is customized, use
+            the `conda: ` parameter to overwrite the default conda environment.
+  - renv: |
+      Optional:
+      Path a folder containing restored `renv` environment or a file within
+      (eg `.Rprofile`, `renv.lock`). If this is used the `renv` must
+      contain a full `quarto` installation.
+      Note that the R version depends on the conda environment used in the wrapper.
+      If this needs to be changed, change the `conda:` parameter to point to an
+      appropriate conda environment.
+      Default: the project root directory
+  - additional_inputs: |
+      Additional input files. These the paths will be passed as `-P <additional_inputs>:<value>` to the quarto script
+      and need to be defined in the quarto header as params: https://quarto.org/docs/computations/parameters.html#knitr
+output:
+  - report: |
+      Optional:
+      Path to the rendered report. The file extension will be used to determine the output format (eg `report.html`, `report.docx`).
+      PDF rendering is currently not supported due to the lack of support of tinytex in conda-forge.
+      If not provided, the report will be rendered in a temporary directory and no output will be returned.
+  - additional_outputs: |
+      Additional output files. These the paths will be passed as `-P <additional_outputs>:<value>` to the quarto script
+      and need to be defined in the quarto header as params: https://quarto.org/docs/computations/parameters.html#knitr
+params:
+  - additional_params: |
+      Additional parameters to be passed to the quarto script. These the paths will be passed as `-P <additional_params>:<value>` to the quarto script
+      and need to be defined in the quarto header as params: https://quarto.org/docs/computations/parameters.html#knitr
+notes: |
+  This wrapper runs quarto to render markdown .qmd notebooks.
+  The wrapper supports r-package management via `conda` and `renv`:
+  - For `conda` overwrite the conda environment from the `conda:` directive of the rule with an environement with
+  the r dependencies as well as `r-quarto` installed.
+  - For `renv` restore an environment before and point the `input.renv`
+  to the environment folder or a file within (eg `.Rprofile`). The r-version needs used to build the `renv` needs to match
+  the one of the wrapper or the environment of the wrapper needs to be overwritten with via `conda:` with a matching `r-base`
+  installation.
+  PDF rendering is currently not working as tinytex is not properly supported in `conda`.
\ No newline at end of file
diff --git a/utils/quarto/test/Snakefile b/utils/quarto/test/Snakefile
new file mode 100644
index 00000000000..3920b4ff887
--- /dev/null
+++ b/utils/quarto/test/Snakefile
@@ -0,0 +1,173 @@
+import os
+
+
+rule all:  # [hide]
+    input:  # [hide]
+        "output/simple.html",  # [hide]
+        "output/resources.html",  # [hide]
+        "output/simple.docx",  # [hide]
+        "output/example_proj_full.html",  # [hide]
+        "output/example_proj_noreport.txt",  # [hide]
+        "output/extra_datatable_renv.html",  # [hide]
+
+
+rule testfile:
+    output:
+        touch("{project}_input.txt"),
+
+
+rule render_quarto_full:
+    input:
+        script="full.qmd",
+        input_txt="{project}_input.txt",
+    output:
+        report="{project}_full.html",
+        output_txt="{project}_output.txt",
+    params:
+        project=lambda wc: wc.project,
+    log:
+        "logs/{project}_html.log",
+    wrapper:
+        "master/utils/quarto"
+
+
+rule render_html:
+    input:
+        script="simple.qmd",
+    output:
+        report="output/simple.html",
+    log:
+        "logs/simple_html.log",
+    wrapper:
+        "master/utils/quarto"
+
+
+rule render_docx:
+    input:
+        script="simple.qmd",
+    output:
+        report="output/simple.docx",
+    log:
+        "logs/simple_docx.log",
+    wrapper:
+        "master/utils/quarto"
+
+
+rule render_quarto_noreport:
+    input:
+        script="full.qmd",
+        input_txt="{project}_input.txt",
+    output:
+        output_txt="{project}_noreport.txt",
+    log:
+        "logs/{project}_noreport.log",
+    wrapper:
+        "master/utils/quarto"
+
+
+rule pass_custom_resources:
+    input:
+        script="resources_custom.qmd",
+    output:
+        report="output/resources_custom.html",
+    resources:
+        custom_resource=1,
+    log:
+        "logs/pass_custom_resources.log",
+    wrapper:
+        "master/utils/quarto"
+
+
+rule pass_threads:
+    input:
+        script="resources_threads.qmd",
+    output:
+        report="output/resources_threads.html",
+    log:
+        "logs/pass_threads.log",
+    wrapper:
+        "master/utils/quarto"
+
+
+# To add additional r-dependencies used to render
+# the report also the conda: directive can be
+# overwritten. The only required dependency
+# is r-quarto
+# rule render_quarto_extra_conda:
+#     conda:
+#         "env/extra.yaml"
+#     input:
+#         script="extra_datatable.qmd",
+#     output:
+#         report="output/extra_datatable_conda.html",
+#     log:
+#         "logs/conda.log",
+#     wrapper:
+#         "master/utils/quarto"
+
+
+# Rules for a example using renv
+wildcard_constraints:
+    # Allows renv_dir also to be the empty (=root dir)
+    renv_dir=".*",
+
+
+# The `renv_lock` on renv rules is an artificial resource to prevent multiple
+# renv operations at the same time, which may cause issues..
+# In such cases restrict it via the
+# resources CLI flag: --resources renv_lock=1 --set-resource-scopes renv_lock=global
+
+
+rule renv_example_init:
+    conda:
+        "env/renv.yaml"
+    input:
+        lockfile="env/renv_dt.lock",
+    output:
+        rprofile="{renv_dir}/.Rprofile",
+        lockfile="{renv_dir}/renv.lock",
+    resources:
+        renv_lock=1,
+    log:
+        "logs/renv/{renv_dir}_init.log",
+    shell:
+        """
+        Rscript -e "renv::init(project='{wildcards.renv_dir}', bare=T); \
+                    renv::restore(project='{wildcards.renv_dir}', lockfile='$(realpath {input.lockfile})');\
+                    renv::snapshot(type='all')"
+        """
+
+
+rule restore_renv:
+    conda:
+        "env/renv.yaml"
+    input:
+        rprofile="{renv_dir}.Rprofile",
+        lock="{renv_dir}renv.lock",
+    output:
+        restored="{renv_dir}restored.Rprofile",
+    resources:
+        renv_lock=1,
+    log:
+        "logs/renv/{renv_dir}_restore.log",
+    shell:
+        """
+        R -e 'source("{input.rprofile}", chdir=TRUE);renv::restore()'
+        echo 'source("{input.rprofile}", chdir=TRUE)' > {output.restored}
+        """
+
+
+rule render_quarto_renv:
+    # If the renv is build using a different r version
+    # than the wrapper, the "conda:" directive may can be overwritten
+    # using an environment with the correct "r-base" & "r-conda"
+    # installed
+    input:
+        script="extra_datatable.qmd",
+        renv="env/renv_test/restored.Rprofile",
+    output:
+        report="output/extra_datatable_renv.html",
+    log:
+        "logs/renv.log",
+    wrapper:
+        "master/utils/quarto"
diff --git a/utils/quarto/test/env/renv.linux-64.pin.txt b/utils/quarto/test/env/renv.linux-64.pin.txt
new file mode 100644
index 00000000000..a1a3b84cb6e
--- /dev/null
+++ b/utils/quarto/test/env/renv.linux-64.pin.txt
@@ -0,0 +1,92 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_17.conda#d731b543793afc0433c4fd593e693fce
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74
+https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.2.0-hdb50d1a_111.conda#43178c27fac2dcd495bd9e58e18272d9
+https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-hdb50d1a_111.conda#4ffa92ea4ba6555dee156ce3d0ae7a9b
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_11.conda#8c462ced2af33648195dc9459f331f31
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda#595db67e32b276298ff3d94d07d47fbf
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_7.conda#3f840c7ed70a96b5ebde8044b2f36f32
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_11.conda#0b3b218a596bb4c3854cc9ee799f94e5
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
+https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79
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+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559
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+https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a
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+https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_1003.conda#bce9f945da8ad2ae9b1d7165a64d0f87
+https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2#b4a4381d54784606820704f7b5f05a15
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61
+https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c
+https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff
+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f
+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_11.conda#4c3e460d6acf8e43e4ce8bf405187eb7
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
+https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae
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+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
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+https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.44-h0f59acf_0.conda#3914f7ac1761dce57102c72ca7c35d01
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+https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.4-h7391055_0.conda#93ee23f12bc2e684548181256edd2cf6
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
+https://conda.anaconda.org/conda-forge/linux-64/bwidget-1.9.14-ha770c72_1.tar.bz2#5746d6202ba2abad4a4707f2a2462795
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+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
+https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.2-h8a4344b_1.conda#9c406bb3d4dac2b358873e6462496d09
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155
+https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504
+https://conda.anaconda.org/conda-forge/linux-64/tktable-2.10-h0c5db8f_5.conda#9464044754ea25557a9c93f0327d90a6
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-hb711507_1.conda#4a6d410296d7e39f00bacdee7df046e9
+https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d
+https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-13.2.0-h9efe08d_11.conda#d08f638bb8b62d71f2222ecb7003a995
+https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-13.2.0-h2a599c4_11.conda#c2f0227c9bea564b8edc2f1de939c76d
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+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb
+https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hbb29018_1.conda#e31a51ddd52326d10a9cc50b0d68daab
+https://conda.anaconda.org/conda-forge/linux-64/curl-8.8.0-he654da7_0.conda#042341d8b9ba4ee7f2722b81fae9f0ad
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-22_linux64_openblas.conda#b083767b6c877e24ee597d93b87ab838
+https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.5.0-hfac3d4d_0.conda#f5126317dd0ce0ba26945e411ecc6960
+https://conda.anaconda.org/conda-forge/linux-64/pango-1.54.0-h84a9a3c_0.conda#7c51e110b2f059c0843269d3324e4b22
+https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-h8ee917f_2.conda#fdd20aea0c8243bfa7fb85d144f4febe
+https://conda.anaconda.org/conda-forge/noarch/r-renv-1.0.7-r43hc72bb7e_0.conda#efa116dc4d7118a48c97f6f8f4861427
diff --git a/utils/quarto/test/env/renv.yaml b/utils/quarto/test/env/renv.yaml
new file mode 100644
index 00000000000..23355a5c8b1
--- /dev/null
+++ b/utils/quarto/test/env/renv.yaml
@@ -0,0 +1,6 @@
+channels:
+    - conda-forge
+    - nodefaults
+dependencies:
+    - r-base=4.3.3
+    - r-renv=1.0.7
\ No newline at end of file
diff --git a/utils/quarto/test/env/renv_dt.lock b/utils/quarto/test/env/renv_dt.lock
new file mode 100644
index 00000000000..13c0acdebee
--- /dev/null
+++ b/utils/quarto/test/env/renv_dt.lock
@@ -0,0 +1,418 @@
+{
+  "R": {
+    "Version": "4.3.3",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cloud.r-project.org"
+      }
+    ]
+  },
+  "Packages": {
+    "R6": {
+      "Package": "R6",
+      "Version": "2.5.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+    },
+    "Rcpp": {
+      "Package": "Rcpp",
+      "Version": "1.0.12",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "methods",
+        "utils"
+      ],
+      "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
+    },
+    "base64enc": {
+      "Package": "base64enc",
+      "Version": "0.1-3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "543776ae6848fde2f48ff3816d0628bc"
+    },
+    "bslib": {
+      "Package": "bslib",
+      "Version": "0.7.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "cachem",
+        "fastmap",
+        "grDevices",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "lifecycle",
+        "memoise",
+        "mime",
+        "rlang",
+        "sass"
+      ],
+      "Hash": "8644cc53f43828f19133548195d7e59e"
+    },
+    "cachem": {
+      "Package": "cachem",
+      "Version": "1.1.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "fastmap",
+        "rlang"
+      ],
+      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
+    },
+    "cli": {
+      "Package": "cli",
+      "Version": "3.6.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
+    },
+    "data.table": {
+      "Package": "data.table",
+      "Version": "1.15.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e"
+    },
+    "digest": {
+      "Package": "digest",
+      "Version": "0.6.35",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
+    },
+    "evaluate": {
+      "Package": "evaluate",
+      "Version": "0.24.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "a1066cbc05caee9a4bf6d90f194ff4da"
+    },
+    "fastmap": {
+      "Package": "fastmap",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
+    },
+    "fontawesome": {
+      "Package": "fontawesome",
+      "Version": "0.5.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "rlang"
+      ],
+      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
+    },
+    "fs": {
+      "Package": "fs",
+      "Version": "1.6.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
+    },
+    "glue": {
+      "Package": "glue",
+      "Version": "1.7.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "e0b3a53876554bd45879e596cdb10a52"
+    },
+    "highr": {
+      "Package": "highr",
+      "Version": "0.11",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "xfun"
+      ],
+      "Hash": "d65ba49117ca223614f71b60d85b8ab7"
+    },
+    "htmltools": {
+      "Package": "htmltools",
+      "Version": "0.5.8.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "digest",
+        "fastmap",
+        "grDevices",
+        "rlang",
+        "utils"
+      ],
+      "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
+    },
+    "jquerylib": {
+      "Package": "jquerylib",
+      "Version": "0.1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "htmltools"
+      ],
+      "Hash": "5aab57a3bd297eee1c1d862735972182"
+    },
+    "jsonlite": {
+      "Package": "jsonlite",
+      "Version": "1.8.8",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "methods"
+      ],
+      "Hash": "e1b9c55281c5adc4dd113652d9e26768"
+    },
+    "knitr": {
+      "Package": "knitr",
+      "Version": "1.47",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "evaluate",
+        "highr",
+        "methods",
+        "tools",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "7c99b2d55584b982717fcc0950378612"
+    },
+    "later": {
+      "Package": "later",
+      "Version": "1.3.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "Rcpp",
+        "rlang"
+      ],
+      "Hash": "a3e051d405326b8b0012377434c62b37"
+    },
+    "lifecycle": {
+      "Package": "lifecycle",
+      "Version": "1.0.4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "rlang"
+      ],
+      "Hash": "b8552d117e1b808b09a832f589b79035"
+    },
+    "memoise": {
+      "Package": "memoise",
+      "Version": "2.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "cachem",
+        "rlang"
+      ],
+      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
+    },
+    "mime": {
+      "Package": "mime",
+      "Version": "0.12",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "tools"
+      ],
+      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
+    },
+    "processx": {
+      "Package": "processx",
+      "Version": "3.8.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "ps",
+        "utils"
+      ],
+      "Hash": "0c90a7d71988856bad2a2a45dd871bb9"
+    },
+    "ps": {
+      "Package": "ps",
+      "Version": "1.7.6",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "dd2b9319ee0656c8acf45c7f40c59de7"
+    },
+    "quarto": {
+      "Package": "quarto",
+      "Version": "1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "jsonlite",
+        "later",
+        "processx",
+        "rlang",
+        "rmarkdown",
+        "rstudioapi",
+        "tools",
+        "utils",
+        "yaml"
+      ],
+      "Hash": "c94c271f9b998d116186a78b2a9b23c1"
+    },
+    "rappdirs": {
+      "Package": "rappdirs",
+      "Version": "0.3.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
+    },
+    "renv": {
+      "Package": "renv",
+      "Version": "1.0.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "397b7b2a265bc5a7a06852524dabae20"
+    },
+    "rlang": {
+      "Package": "rlang",
+      "Version": "1.1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
+    },
+    "rmarkdown": {
+      "Package": "rmarkdown",
+      "Version": "2.27",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bslib",
+        "evaluate",
+        "fontawesome",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "knitr",
+        "methods",
+        "tinytex",
+        "tools",
+        "utils",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "27f9502e1cdbfa195f94e03b0f517484"
+    },
+    "rstudioapi": {
+      "Package": "rstudioapi",
+      "Version": "0.16.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "96710351d642b70e8f02ddeb237c46a7"
+    },
+    "sass": {
+      "Package": "sass",
+      "Version": "0.4.9",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R6",
+        "fs",
+        "htmltools",
+        "rappdirs",
+        "rlang"
+      ],
+      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
+    },
+    "tinytex": {
+      "Package": "tinytex",
+      "Version": "0.51",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "xfun"
+      ],
+      "Hash": "d44e2fcd2e4e076f0aac540208559d1d"
+    },
+    "xfun": {
+      "Package": "xfun",
+      "Version": "0.45",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "grDevices",
+        "stats",
+        "tools"
+      ],
+      "Hash": "ca59c87fe305b16a9141a5874c3a7889"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.8",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "29240487a071f535f5e5d5a323b7afbd"
+    }
+  }
+}
diff --git a/utils/quarto/test/extra_datatable.qmd b/utils/quarto/test/extra_datatable.qmd
new file mode 100644
index 00000000000..0c724a0d4f7
--- /dev/null
+++ b/utils/quarto/test/extra_datatable.qmd
@@ -0,0 +1,15 @@
+---
+title: "Quarto example with additional package dependency"
+author: "Vito Zanotelli, University Children's Hospital Zurich"
+format: html
+---
+
+This quarto markdown is used to demonstrate how an extra
+dependency - 'data.table' can be installed either via conda or renv.
+
+As 'data.table' is not available in the base environment, building
+this report fails if it has not been additionally installed.
+
+```{r, Try to load data table}
+library(data.table)
+```
diff --git a/utils/quarto/test/full.qmd b/utils/quarto/test/full.qmd
new file mode 100644
index 00000000000..c7a55a55495
--- /dev/null
+++ b/utils/quarto/test/full.qmd
@@ -0,0 +1,15 @@
+---
+title: "Full Quarto example: `r params$project`"
+author: "Vito Zanotelli, University Children's Hospital Zurich"
+format: html
+params:
+  input_txt: '../results/test.txt'
+  output_txt: '../results/test_copy.txt'
+  project: 'Test'
+---
+
+
+```{r}
+#| label: copy example file
+file.copy(params$input_txt, params$output_txt)
+```
diff --git a/utils/quarto/test/resources_custom.qmd b/utils/quarto/test/resources_custom.qmd
new file mode 100644
index 00000000000..ddda5d745e6
--- /dev/null
+++ b/utils/quarto/test/resources_custom.qmd
@@ -0,0 +1,15 @@
+---
+title: "Quarto resource passing example"
+author: "Vito Zanotelli, University Children's Hospital Zurich"
+format: html
+params:
+  resources_custom_resource: NULL
+---
+
+
+```{r}
+#| label: Verify that resource custom_resource is passed
+if (is.null(params$resources_custom_resource)){
+  stop('resource "custom_resource" not passed to report')
+}
+```
\ No newline at end of file
diff --git a/utils/quarto/test/resources_threads.qmd b/utils/quarto/test/resources_threads.qmd
new file mode 100644
index 00000000000..d3ab453ca26
--- /dev/null
+++ b/utils/quarto/test/resources_threads.qmd
@@ -0,0 +1,16 @@
+---
+title: "Quarto resource passing example"
+author: "Vito Zanotelli, University Children's Hospital Zurich"
+format: html
+params:
+  resources_threads: NULL
+---
+
+
+```{r}
+#| label: Verify that threads are passed
+if (is.null(params$resources_threads)){
+  stop('resource "threads" not passed to report')
+}
+```
+
diff --git a/utils/quarto/test/simple.qmd b/utils/quarto/test/simple.qmd
new file mode 100644
index 00000000000..eab3afb7372
--- /dev/null
+++ b/utils/quarto/test/simple.qmd
@@ -0,0 +1,7 @@
+---
+title: "Quarto example"
+author: "Vito Zanotelli, University Children's Hospital Zurich"
+format: html
+---
+
+Hello Quarto!
\ No newline at end of file
diff --git a/utils/quarto/wrapper.py b/utils/quarto/wrapper.py
new file mode 100644
index 00000000000..871a2a12dc6
--- /dev/null
+++ b/utils/quarto/wrapper.py
@@ -0,0 +1,159 @@
+__author__ = "Vito Zanotelli"
+__copyright__ = "Copyright 2024, Vito Zanotelli"
+__email__ = "vito.zanotelli@kispi.uzh.ch"
+__license__ = "MIT"
+
+import tempfile
+from pathlib import Path
+import warnings
+import yaml
+from snakemake.shell import shell
+
+
+def parse_renv(renv_path: Path) -> str:
+    """Parse the renv path
+
+    Args:
+        renv_path (Path): A path to an renv folder
+            or a file in the renv folder
+
+    Returns:
+        str: the resolved path pointing to the
+            renv folder
+    """
+    if renv_path.is_file():
+        renv_path = renv_path.parent
+    return str(renv_path.resolve())
+
+
+def parse_qmd_header(fn_script):
+    """Parse the yml header of the a
+    quarto markdown file
+
+    Args:
+        fn_script (path): Path to the qmd script
+
+    Raises:
+        ValueError: qmd has not valid header
+
+    Returns:
+        dict: parsed header
+    """
+    with open(fn_script, mode="r") as f:
+        first = f.readline()
+        if first != "---\n":
+            raise ValueError(".qmd file has no valid yaml header.")
+        line = f.readline()
+        yml_lines = []
+        while line != "---\n":
+            yml_lines.append(line)
+            line = f.readline()
+    return yaml.safe_load("".join(yml_lines))
+
+
+def add_parameter(name: str, value, param_list: list[str]) -> None:
+    """Add a parameter to the parameter list in place
+
+    Args:
+        name (str): The name of the parameter
+        value (str): The value of the parameter
+        param_list (list[str]): The list of parameters
+
+    Returns:
+        None
+    """
+    if isinstance(value, list):
+        value = ",".join(value)
+    param_list.append("-P {}:{}".format(name, value))
+
+
+renv = parse_renv(Path(snakemake.input.get("renv", ".")))
+script = Path(snakemake.input.get("script"))
+report = snakemake.output.get("report", None)
+
+
+# Build params to be passed to Quarto params (-P flag)
+params = []
+for name, value in snakemake.input.items():
+    if name not in {"renv", "script"}:
+        add_parameter(name, value, params)
+
+for name, value in snakemake.params.items():
+    add_parameter(name, value, params)
+
+for name, value in snakemake.output.items():
+    if name not in {"report"}:
+        add_parameter(name, value, params)
+
+
+# Get the snakemake resources that correspond to
+# Params in the qmd header that are prefixed with the resource prefix
+# RESOURCE_PARAMS_PREFIX.
+# eg resources_mem -> snakemake.resources.mem
+RESOURCE_PARAMS_PREFIX = "resources_"
+params_header = parse_qmd_header(script).get("params", {})
+resources = {**snakemake.resources}
+resources["threads"] = snakemake.threads
+passed_resource_params = {
+    f"{RESOURCE_PARAMS_PREFIX}{k}": v
+    for k, v in resources.items()
+    if f"{RESOURCE_PARAMS_PREFIX}{k}" in params_header.keys()
+}
+
+for name, value in passed_resource_params.items():
+    add_parameter(name, value, params)
+
+
+# Resolve the logfile path and set the log_fmt_shell
+# This is required as we may change the working directory
+# to the renv folder for execution of quarto.
+logfile = snakemake.log
+if logfile:
+    snakemake.log = str(Path(str(logfile)).resolve())
+    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+else:
+    log = ""
+
+args = " ".join(params)
+
+with tempfile.TemporaryDirectory() as temp_output:
+    if report is None:
+        # In case no report output is specified,
+        # the output is created in a temporary folder
+        out_report = Path(temp_output) / script.name
+        out_report_rendered = out_report
+        report_path = f"{out_report}.tmp"
+    else:
+        # In case an output is specified,
+        # the output is created in the target folder.
+        report_path = Path(report).resolve()
+        # The report to-be-rendered is namespaced
+        # to prevent clashes.
+        out_report = (
+            report_path.parent / f"{report_path.stem}_{report_path.suffix[1:]}.qmd"
+        )
+        # The rendered report is named as the final report with the correct suffix
+        # Note that in addition ot the target report file, also a folder `*_files/`
+        # is created, which contains the images and other files linked in the html report.
+        out_report_rendered = out_report.with_suffix(report_path.suffix)
+        if report_path.suffix == ".pdf":
+            warnings.warn(
+                "PDF output is likely not supported yet, as tinytex not installable"
+                " via conda: https://github.com/conda-forge/quarto-feedstock/issues/26"
+            )
+        args += f" --to={report_path.suffix[1:]}"
+    shell(
+        """
+        # copy the input script to prevent name clashes
+        cp {script} {out_report}
+        WD=$(pwd)
+        # Change to renv directory to enable the renv
+        cd "{renv}"
+        quarto render {out_report} \
+                {args} \
+                --execute-dir="$WD" \
+          {log}
+        # move the output to the final destination
+        mv {out_report_rendered} {report_path}
+        """
+    )