diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..ff16024
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,34 @@
+on:
+  push:
+    branches:
+      - main
+
+name: Release
+
+jobs:
+  bump-version:
+    name: Release version
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: GoogleCloudPlatform/release-please-action@v3
+        id: release
+        with:
+          release-type: python # just keep a changelog, no version anywhere outside of git tags
+          package-name: juno_template
+  lint:
+    name: Lint Code Base
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+
+      - name: Lint Code Base
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: main
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+          VALIDATE_SNAKEMAKE_SNAKEFMT: true
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..a151261
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,144 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Vscode stuff:
+.vscode
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Added stuff
+.snakemake
+envs/src
+input
+output
+sample_sheet.yaml
+config/sample_sheet.yaml
+config/variables.yaml
+config/juno_call.txt 
+config/user_parameters.yaml
+core.*
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..f73a69e
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "juno-library"]
+	path = base_juno_pipeline
+	url = https://github.com/RIVM-bioinformatics/base_juno_pipeline.git
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..7558497
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,8 @@
+# Changelog
+
+## [1.0.1](https://github.com/RIVM-bioinformatics/juno-template/compare/v1.0.0...v1.0.1) (2023-07-12)
+
+
+### Dependencies
+
+* remove anaconda and defaults and add no defaults channel ([0b4fccb](https://github.com/RIVM-bioinformatics/juno-template/commit/0b4fccb29d192570060ed81f6222b78293e195a7))
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..a4802bc
--- /dev/null
+++ b/README.md
@@ -0,0 +1,7 @@
+# Juno-Template
+A template pipeline where the other juno pipelines are based on.
+
+## Contribution guidelines
+Juno pipelines use a [feature branch workflow](https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow). To work on features, create a branch from the `main` branch to make changes to. This branch can be merged to the main branch via a pull request. Hotfixes for bugs can be committed to the `main` branch.
+
+Please adhere to the [conventional commits](https://www.conventionalcommits.org/) specification for commit messages. These commit messages can be picked up by [release please](https://github.com/googleapis/release-please) to create meaningful release messages.
diff --git a/Snakefile b/Snakefile
new file mode 100644
index 0000000..cd1fde2
--- /dev/null
+++ b/Snakefile
@@ -0,0 +1,25 @@
+import yaml
+
+
+sample_sheet=config["sample_sheet"]
+with open(sample_sheet) as f:
+    SAMPLES = yaml.safe_load(f)
+
+for param in ["threads", "mem_gb"]:
+    for k in config[param]:
+        config[param][k] = int(config[param][k])
+
+# print(SAMPLES)
+
+OUT = config["output_dir"]
+
+localrules:
+    all,
+
+
+include: "workflow/rules/rule.smk"
+
+
+rule all:
+    input:
+        expand(OUT + "/{sample}_combined.fastq", sample=SAMPLES),
diff --git a/base_juno_pipeline b/base_juno_pipeline
new file mode 160000
index 0000000..3d05d8b
--- /dev/null
+++ b/base_juno_pipeline
@@ -0,0 +1 @@
+Subproject commit 3d05d8bd7f0010547e3ac5a2d8751a000f44dffb
diff --git a/config/pipeline_parameters.yaml b/config/pipeline_parameters.yaml
new file mode 100644
index 0000000..d240a8f
--- /dev/null
+++ b/config/pipeline_parameters.yaml
@@ -0,0 +1,5 @@
+threads:
+    template_rule: 1
+
+mem_gb:
+    template_rule: 1
diff --git a/envs/mamba.yaml b/envs/mamba.yaml
new file mode 100644
index 0000000..57a4e0e
--- /dev/null
+++ b/envs/mamba.yaml
@@ -0,0 +1,5 @@
+name: mamba
+channels:
+  - conda-forge
+dependencies:
+  - mamba
diff --git a/envs/template_master.yaml b/envs/template_master.yaml
new file mode 100644
index 0000000..9ca076d
--- /dev/null
+++ b/envs/template_master.yaml
@@ -0,0 +1,15 @@
+name: juno_template
+channels:
+  - conda-forge
+  - bioconda
+  - biocore
+  - nodefaults
+dependencies:
+  - git=2.40.*
+  - mamba=1.3.*
+  - pandas=1.5.*
+  - snakemake=7.18.*
+  - pip=23.*
+  - python=3.11.*
+  - pip:
+    - "--editable=git+https://github.com/RIVM-bioinformatics/juno-library.git@v2.0.0#egg=juno_library"
diff --git a/run_pipeline.sh b/run_pipeline.sh
new file mode 100755
index 0000000..56cb9f6
--- /dev/null
+++ b/run_pipeline.sh
@@ -0,0 +1,86 @@
+#!/bin/bash
+
+set -euo pipefail
+
+#----------------------------------------------#
+# User parameters
+if [ ! -z "${1}" ] || [ ! -z "${2}" ] #|| [ ! -z "${irods_input_projectID}" ]
+then
+   input_dir="${1}"
+   output_dir="${2}"
+#    PROJECT_NAME="${irods_input_projectID}"
+else
+    echo "One of the parameters is missing, make sure there is an input directory, output directory and project name(param 1, 2 or irods_input_projectID)."
+    exit 1
+fi
+
+if [ ! -d "${input_dir}" ] || [ ! -d "${output_dir}" ]
+then
+  echo "The input directory $input_dir, output directory $output_dir or fastq dir ${input_dir}/clean_fastq does not exist"
+  exit 1
+else
+  input_fastq="${input_dir}/clean_fastq"
+fi
+
+#----------------------------------------------#
+# Create/update necessary environments
+PATH_MAMBA_YAML="envs/mamba.yaml"
+PATH_MASTER_YAML="envs/template_master.yaml"
+MAMBA_NAME=$(head -n 1 ${PATH_MAMBA_YAML} | cut -f2 -d ' ')
+MASTER_NAME=$(head -n 1 ${PATH_MASTER_YAML} | cut -f2 -d ' ')
+
+echo -e "\nUpdating necessary environments to run the pipeline..."
+
+# Removing strict mode because it sometimes breaks the code for 
+# activating an environment and for testing whether some variables
+# are set or not
+set +euo pipefail 
+
+conda env update -f "${PATH_MAMBA_YAML}"
+source activate "${MAMBA_NAME}"
+
+mamba env update -f "${PATH_MASTER_YAML}"
+
+source activate "${MASTER_NAME}"
+
+#----------------------------------------------#
+# Run the pipeline
+
+echo -e "\nRun pipeline..."
+
+if [ ! -z ${irods_runsheet_sys__runsheet__lsf_queue} ]; then
+    QUEUE="${irods_runsheet_sys__runsheet__lsf_queue}"
+else
+    QUEUE="bio"
+fi
+
+set -euo pipefail
+
+python template.py --queue "${QUEUE}" -i "${input_dir}" -o "${output_dir}"
+
+result=$?
+
+# Propagate metadata
+
+set +euo pipefail
+
+SEQ_KEYS=
+SEQ_ENV=`env | grep irods_input_sequencing`
+for SEQ_AVU in ${SEQ_ENV}
+do
+    SEQ_KEYS="${SEQ_KEYS} ${SEQ_AVU%%=*}"
+done
+
+for key in $SEQ_KEYS irods_input_illumina__Flowcell irods_input_illumina__Instrument \
+    irods_input_illumina__Date irods_input_illumina__Run_number irods_input_illumina__Run_Id
+do
+    if [ ! -z ${!key} ] ; then
+        attrname=${key:12}
+        attrname=${attrname/__/::}
+        echo "${attrname}: '${!key}'" >> ${OUTPUTDIR}/metadata.yml
+    fi
+done
+
+set -euo pipefail
+
+exit ${result}
diff --git a/template.py b/template.py
new file mode 100644
index 0000000..36724d2
--- /dev/null
+++ b/template.py
@@ -0,0 +1,85 @@
+"""
+Juno template
+Authors: Karim Hajji, Roxanne Wolthuis
+Organization: Rijksinstituut voor Volksgezondheid en Milieu (RIVM)
+Department: Infektieziekteonderzoek, Diagnostiek en Laboratorium
+            Surveillance (IDS), Bacteriologie (BPD)     
+Date: 05-04-2023   
+"""
+
+from pathlib import Path
+import pathlib
+import yaml
+import argparse
+import sys
+from dataclasses import dataclass, field
+from juno_library import Pipeline
+from typing import Optional
+from version import __package_name__, __version__, __description__
+
+def main() -> None:
+    juno_template = JunoTemplate()
+    juno_template.run()
+
+@dataclass
+class JunoTemplate(Pipeline):
+    pipeline_name: str = __package_name__
+    pipeline_version: str = __version__
+    input_type: str = "fastq"
+
+    def _add_args_to_parser(self) -> None:
+        super()._add_args_to_parser()
+
+        self.parser.description = "Template juno pipeline. If you see this message please change it to something appropriate"
+        
+        self.add_argument(
+            "--example-option",
+            dest="example",
+            type=str,
+            required=False,
+            metavar="STR",
+            help="This is an optional argument, specific for this pipeline. General options are included in juno-library.",
+        )
+        
+    def _parse_args(self) -> argparse.Namespace:
+        args = super()._parse_args()
+
+        # Optional arguments are loaded into self here
+        self.example: bool = args.example
+
+        return args
+    
+    # Extra class methods for this pipeline can be defined here
+    def example_class_method(self):
+        print(f"example option is set to {self.example}")
+
+    def setup(self) -> None:
+        super().setup()
+
+        if self.snakemake_args["use_singularity"]:
+            self.snakemake_args["singularity_args"] = " ".join(
+                [
+                    self.snakemake_args["singularity_args"]
+                ] # paths that singularity should be able to read from can be bound by adding to the above list
+            )
+
+        # Extra class methods for this pipeline can be invoked here
+        if self.example:
+            self.example_class_method()
+
+        with open(
+            Path(__file__).parent.joinpath("config/pipeline_parameters.yaml")
+        ) as f:
+            parameters_dict = yaml.safe_load(f)
+        self.snakemake_config.update(parameters_dict)
+
+        self.user_parameters = {
+            "input_dir": str(self.input_dir),
+            "output_dir": str(self.output_dir),
+            "exclusion_file": str(self.exclusion_file),
+            "example": str(self.example), # other user parameters can be included in user_parameters.yaml here
+        }
+
+
+if __name__ == "__main__":
+    main()
diff --git a/version.py b/version.py
new file mode 100644
index 0000000..e5d8a19
--- /dev/null
+++ b/version.py
@@ -0,0 +1,6 @@
+__package_name__ = "juno_template"
+__authors__ = "author"
+__email__ = "author@rivm.nl"
+__license__ = "AGPLv3"
+__version__ = "1.0"
+__description__ = "Template juno pipeline. If you see this message please change it to something appropriate"
\ No newline at end of file
diff --git a/workflow/envs/env.yaml b/workflow/envs/env.yaml
new file mode 100644
index 0000000..e69de29
diff --git a/workflow/rules/rule.smk b/workflow/rules/rule.smk
new file mode 100644
index 0000000..1730f76
--- /dev/null
+++ b/workflow/rules/rule.smk
@@ -0,0 +1,17 @@
+rule template_rule:
+    input:
+        lambda wc: SAMPLES[wc.sample]["R1"],
+        lambda wc: SAMPLES[wc.sample]["R2"],
+    output:
+        OUT + "/{sample}_combined.fastq",
+    log:
+        OUT + "/log/{sample}_template_rule.log"
+    message:
+        "Merging {input}."
+    resources:
+        mem_gb=config["mem_gb"]["template_rule"],
+    params: script = "workflow/scripts/script.py"
+    threads: config["threads"]["template_rule"]
+    shell: """
+    python {params.script} {input} > {output}
+    """
diff --git a/workflow/scripts/script.py b/workflow/scripts/script.py
new file mode 100644
index 0000000..81656b6
--- /dev/null
+++ b/workflow/scripts/script.py
@@ -0,0 +1,6 @@
+import subprocess
+import sys
+
+subprocess.call(
+    ["cat"] + sys.argv[1:],
+)