diff --git a/.github/workflows/apptainer.yml b/.github/workflows/apptainer.yml
new file mode 100644
index 0000000..7cf8cab
--- /dev/null
+++ b/.github/workflows/apptainer.yml
@@ -0,0 +1,61 @@
+name: Apptainer Run
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches-ignore: []
+  schedule:
+    - cron: '0 0 * * SUN'
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+      matrix:
+        python: [3.8, '3.10']
+      fail-fast: false
+
+
+    steps:
+
+    - name: precleanup
+      run: |
+        sudo rm -rf /usr/share/dotnet
+        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+    - name: install graphviz
+      run: |
+        sudo apt update
+        sudo apt-get install -y graphviz software-properties-common
+        sudo add-apt-repository -y ppa:apptainer/ppa
+        sudo apt update
+        sudo apt install -y apptainer
+
+    - name: checkout git repo
+      uses: actions/checkout@v3
+
+    - name: Set up Python 3.X
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python }}
+
+    - name: Install dependencies
+      run: |
+        pip install .[testing]
+
+    - name: install package itself
+      run: |
+         pip install .
+
+    - name: testing
+      run: |
+
+        sequana_ribofinder --input-directory test/data --reference-file test/data/Lepto.fa --gff-file test/data/Lepto.gff --use-apptainer && cd ribofinder && sh ribofinder.sh
+
+
+
+
+
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0b3a5f4..bd3788a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -3,9 +3,13 @@ name: Tests
 on:
   push:
     branches:
-      - master
+      - main
+      - dev
+  workflow_dispatch:
   pull_request:
     branches-ignore: []
+  schedule:
+    - cron: '0 0 2 * *'
 
 jobs:
   build-linux:
@@ -13,47 +17,47 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.7,3.8,3.9]
+        python: ['3.11', '3.12']
       fail-fast: false
 
+
     steps:
 
     - name: install graphviz
       run: |
+        sudo apt-get update -qq
         sudo apt-get install -y graphviz
 
     - name: checkout git repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
-    - name: Set up Python 3.X
-      uses: actions/setup-python@v2
+    - name: conda/mamba
+      uses: mamba-org/setup-micromamba@v2
       with:
-        python-version: ${{ matrix.python }}
-
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-        conda update ruamel_yaml
+          environment-file: environment.yml
+          create-args: >-
+            python=${{ matrix.python }}
+          cache-environment: true
+          cache-downloads: true
 
-    - name: conda
+    - name: install package itself
+      shell: bash -l {0}
       run: |
-        conda install -c conda-forge --quiet mamba  python=${{ matrix.python }}
-        mamba install -c bioconda -c conda-forge --quiet -y bowtie samtools bamtools pigz bedtools
+        pip install .
 
     - name: Install dependencies
+      shell: bash -l {0}
       run: |
         pip install coveralls pytest-cov pytest pytest-xdist
 
-    - name: install package itself
-      run: |
-         pip install .
-
     - name: testing
+      shell: bash -l {0}
       run: |
         pytest -v --cov-report term-missing --cov=sequana_pipelines.ribofinder
 
     - name: coveralls
+      continue-on-error: true
+      shell: bash -l {0}
       run: |
         echo $COVERALLS_REPO_TOKEN
         coveralls --service=github
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index a13767b..5b1e408 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -8,32 +8,33 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish to PyPI and TestPyPI
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v4
     - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.8
 
-    - name: Install package
+    - name: Install package 
       run: |
-          pip install build
+          pip install build poetry
 
     - name: Build source tarball
       run: |
           rm -rf dist;
-          python setup.py sdist
-
+          poetry build
+ 
     - name: Publish distribution to Test PyPI
+      if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@master
       with:
-        user: __token__
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-        repository_url: https://test.pypi.org/legacy/
+        repository-url: https://test.pypi.org/legacy/
     - name: Publish distribution to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 5219b3c..0000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,5 +0,0 @@
-recursive-exclude * __pycache__
-recursive-exclude * *pyc
-recursive-include * *rules
-include requirements*txt
-include README.rst
diff --git a/README.rst b/README.rst
index 6f0d89d..64e3cd0 100644
--- a/README.rst
+++ b/README.rst
@@ -9,6 +9,10 @@
 .. image:: https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg
    :target: https://github.com/sequana/ribofinder/actions/workflows/main.yml
 
+.. image:: https://img.shields.io/badge/python-3.11%20%7C%203.12-blue.svg
+    :target: https://pypi.python.org/pypi/sequana_ribofinder
+    :alt: Python 3.11 | 3.12
+
 
 This is is the **ribofinder** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
 
@@ -62,8 +66,10 @@ Requirements
 
 This pipelines requires the following executable(s):
 
-- bowtie1
+- bowtie1 >= 1.3.0
+- bedtools
 - samtools
+- bamtools
 - pigz
 
 .. image:: https://raw.githubusercontent.com/sequana/ribofinder/master/sequana_pipelines/ribofinder/dag.png
@@ -102,6 +108,12 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.1.1     * hotfix for running on HPC (slurm)
+1.1.0     * Uses click (refactoring of sequana_pipetools)
+1.0.1     * add sequana_wrappers in the config/pipeline
+1.0.0     * use graphviz apptainer and latest wrappers
+0.13.0    * add  final apptainers and update CI actions
+0.12.0    * set singularity containers
 0.11.1    * Fix config file (removing hard-coded path)
 0.11.0    * Fix multiqc plot using same fix as in sequna_rnaseq pipelines
           * add utility plot to check rate of  ribosomal per sequence and also
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..e30f4d3
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,14 @@
+name: sequana_ribofinder
+
+channels:
+- conda-forge
+- bioconda
+- defaults
+- r
+
+dependencies:
+- 'bowtie>=1.3.0'
+- samtools>1.7
+- bamtools
+- bedtools
+- pigz
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..6e39ead
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,52 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "sequana-ribofinder"
+version = "1.1.1"
+description = "A multi-sample identification of ribosomal content"
+authors = ["Sequana Team"]
+license = "BSD-3"
+repository = "https://github.com/sequana/ribofinder"
+readme = "README.rst"
+keywords = ["snakemake", "ribosomal", "rRNA", "sequana"]
+classifiers = [
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Education",
+        "Intended Audience :: End Users/Desktop",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Operating System :: POSIX :: Linux",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+]
+
+packages = [
+    {include = "sequana_pipelines"}
+]
+
+
+[tool.poetry.dependencies]
+python = ">=3.8,<4.0"
+sequana = ">=0.15.0"
+sequana_pipetools = ">=0.16.0"
+click-completion = "^0.5.2"
+
+
+[tool.poetry.scripts]
+sequana_ribofinder = "sequana_pipelines.ribofinder.main:main"
+
+
+[tool.poetry.group.dev.dependencies]
+black = "^23.7.0"
+pytest = "^7.4.0"
+mock = "^5.1.0"
+pytest-mock = "^3.11.1"
+pytest-cov = "^4.1.0"
+
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index bf9e35a..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-sequana>=0.12.7
-sequana_pipetools>=0.7.1
diff --git a/sequana_pipelines/ribofinder/__init__.py b/sequana_pipelines/ribofinder/__init__.py
index 132e999..6d5f263 100644
--- a/sequana_pipelines/ribofinder/__init__.py
+++ b/sequana_pipelines/ribofinder/__init__.py
@@ -1,6 +1,11 @@
-import pkg_resources
-try:
-    version = pkg_resources.require("sequana_ribofinder")[0].version
-except:
-    version = ">=0.8.0"
+import importlib.metadata as metadata
+
+def get_package_version(package_name):
+    try:
+        version = metadata.version(package_name)
+        return version
+    except metadata.PackageNotFoundError:
+        return f"{package_name} not found"
+
+version = get_package_version("sequana-ribofinder")
 
diff --git a/sequana_pipelines/ribofinder/config.yaml b/sequana_pipelines/ribofinder/config.yaml
index 979ab16..4c7abe8 100644
--- a/sequana_pipelines/ribofinder/config.yaml
+++ b/sequana_pipelines/ribofinder/config.yaml
@@ -7,6 +7,8 @@
 # If input_directory provided, use it otherwise if input_pattern provided,
 # use it, otherwise use input_samples.
 # ============================================================================
+sequana_wrappers: "v23.11.18"
+
 input_directory:
 input_readtag: _R[12]_
 input_pattern: '*fastq.gz'
@@ -37,10 +39,16 @@ general:
     rRNA_file: ''
     rRNA_feature: rRNA
     genbank_file: ''
-    gff_file: 
-    reference_file: 
-
+    gff_file:
+    reference_file:
 
+apptainers:
+    sequana_ribofinder: "https://zenodo.org/record/7348115/files/sequana_ribofinder_0.12.0.img"
+    pigz: "https://zenodo.org/record/7346805/files/pigz_2.4.0.img"
+    bedtools: "https://zenodo.org/record/7346774/files/bedtools_2.30.0.img"
+    samtools: "https://zenodo.org/record/7215278/files/samtools_1.15.0.img"
+    graphviz:  "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
+    multiqc: "https://zenodo.org/record/10205070/files/multiqc_1.16.0.img"
 
 #############################################################################
 # bowtie1_mapping_rna used to align reads against ribosomal RNA
diff --git a/sequana_pipelines/ribofinder/main.py b/sequana_pipelines/ribofinder/main.py
old mode 100755
new mode 100644
index 6cb5b6e..4f19366
--- a/sequana_pipelines/ribofinder/main.py
+++ b/sequana_pipelines/ribofinder/main.py
@@ -1,12 +1,8 @@
-# -*- coding: utf-8 -*-
 #
 #  This file is part of Sequana software
 #
 #  Copyright (c) 2016 - Sequana Development Team
 #
-#  File author(s):
-#      Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
-#
 #  Distributed under the terms of the 3-clause BSD license.
 #  The full license is in the LICENSE file, distributed with this software.
 #
@@ -16,140 +12,141 @@
 ##############################################################################
 import sys
 import os
-import argparse
-import shutil
 import subprocess
+import shutil
+from pathlib import Path
+
+import rich_click as click
+import click_completion
+
+click_completion.init()
 
 from sequana_pipetools.options import *
-from sequana_pipetools.options import before_pipeline
-from sequana_pipetools.misc import Colors
-from sequana_pipetools.info import sequana_epilog, sequana_prolog
 from sequana_pipetools import SequanaManager
-from sequana import logger
 
-col = Colors()
 
 NAME = "ribofinder"
 
-
-class Options(argparse.ArgumentParser):
-    def __init__(self, prog=NAME, epilog=None):
-        usage = col.purple(sequana_prolog.format(**{"name": NAME}))
-        super(Options, self).__init__(usage=usage, prog=prog, description="",
-            epilog=epilog,
-            formatter_class=argparse.ArgumentDefaultsHelpFormatter
-        )
-        # add a new group of options to the parser
-        so = SlurmOptions()
-        so.add_options(self)
-
-        # add a snakemake group of options to the parser
-        so = SnakemakeOptions(working_directory=NAME)
-        so.add_options(self)
-
-        so = InputOptions()
-        so.add_options(self)
-
-        so = GeneralOptions()
-        so.add_options(self)
-
-        pipeline_group = self.add_argument_group("pipeline_general")
-        pipeline_group.add_argument("--aligner", dest="aligner",
-            choices=['bowtie1'], default='bowtie1',
-            help= "a mapper in bowtie")
-        pipeline_group.add_argument("--rRNA-feature",
-            default="rRNA",
-            help="""Feature name corresponding to the rRNA to be identified for QCs""")
-        pipeline_group.add_argument("--rRNA-file",
-            default=None,
-            help="""If you already have the rRNA file, just provide it""")
-        pipeline_group.add_argument("--genbank-file",
-            default=None,
-            help="""genbank. if provided, do not provide gff""")
-        pipeline_group.add_argument("--gff-file",
-            default=None,
-            help="""If provided, do not provide genbank""")
-        pipeline_group.add_argument("--reference-file",
-            default=None,
-            help="""The required referenceto fetch features into""")
-
-
-        self.add_argument("--run", default=False, action="store_true",
-            help="execute the pipeline directly")
-
-    def parse_args(self, *args):
-        args_list = list(*args)
-        if "--from-project" in args_list:
-            if len(args_list)>2:
-                msg = "WARNING [sequana]: With --from-project option, " + \
-                        "pipeline and data-related options will be ignored."
-                print(col.error(msg))
-            for action in self._actions:
-                if action.required is True:
-                    action.required = False
-        options = super(Options, self).parse_args(*args)
-        return options
-
-
-def main(args=None):
-
-    if args is None:
-        args = sys.argv
-
-    # whatever needs to be called by all pipeline before the options parsing
-    before_pipeline(NAME)
-
-    # option parsing including common epilog
-    options = Options(NAME, epilog=sequana_epilog).parse_args(args[1:])
-
+help = init_click(
+    NAME,
+    groups={
+        "Pipeline Specific": [
+            "--aligner",
+            "--genbank-file",
+            "--gff-file",
+            "--rRNA-feature",
+            "--rRNA-file",
+            "--reference-file",
+        ],
+    },
+)
+
+
+@click.command(context_settings=help)
+@include_options_from(ClickSnakemakeOptions, working_directory=NAME)
+@include_options_from(ClickSlurmOptions)
+@include_options_from(ClickInputOptions)
+@include_options_from(ClickGeneralOptions)
+@click.option(
+    "--aligner", "aligner", type=click.Choice(["bowtie1"]), default="bowtie1", help="the alignement tool (bowtie1)"
+)
+@click.option(
+    "--rRNA-feature",
+    "rRNA_feature",
+    default="rRNA",
+    type=click.STRING,
+    help="""Feature name corresponding to the rRNA to be identified for QCs""",
+)
+@click.option(
+    "--rRNA-file",
+    "rRNA_file",
+    default=None,
+    type=click.Path(file_okay=True, dir_okay=False),
+    help="""If you already have the rRNA file, just provide it""",
+)
+@click.option("--genbank-file", default=None, help="""genbank. if provided, do not provide gff""")
+@click.option("--gff-file", default=None, help="""If provided, do not provide genbank""")
+@click.option("--reference-file", default=None, help="""The required referenceto fetch features into""")
+def main(**options):
     # the real stuff is here
     manager = SequanaManager(options, NAME)
 
     # create the beginning of the command and the working directory
     manager.setup()
 
+    # aliases
+    options = manager.options
+    cfg = manager.config.config
+
+    # fills input_data, input_directory, input_readtag
+    # needs an update of sequana_pipetools to exclude readtag
+    manager.fill_data_options()
+
     # fill the config file with input parameters
-    if options.from_project is None:
-        cfg = manager.config.config
 
-        # --------------------------------------------------------- general
+    # --------------------------------------------------------- general
+    def fill_aligner():
         cfg.general.aligner = options.aligner
 
+    def fill_rRNA_feature():
         cfg.general.rRNA_feature = options.rRNA_feature
+
+    def fill_rRNA_file():
         if options.rRNA_file:
             cfg.general.rRNA_file = os.path.abspath(options.rRNA_file)
+
+    def fill_genbank_file():
         if options.genbank_file:
             cfg.general.genbank_file = os.path.abspath(options.genbank_file)
+
+    def fill_gff_file():
         if options.gff_file:
             cfg.general.gff_file = os.path.abspath(options.gff_file)
+
+    def fill_reference_file():
         if options.reference_file:
             cfg.general.reference_file = os.path.abspath(options.reference_file)
 
+    if options["from_project"]:
+        if "--aligner" in sys.argv:
+            fill_aligner()
+        if "--rRNA-feature" in sys.argv:
+            fill_rRNA_feature()
+        if "--rRNA-file" in sys.argv:
+            fill_rRNA_file()
+        if "--genbank-file" in sys.argv:
+            fill_genbank_file()
+        if "--gff-file" in sys.argv:
+            fill_gff_file()
+        if "--reference-fle" in sys.argv:
+            fill_reference_file()
+
+    else:
+        fill_aligner()
+        fill_rRNA_feature()
+        fill_rRNA_file()
+        fill_genbank_file()
+        fill_gff_file()
+        fill_reference_file()
+
         if options.reference_file is None and options.rRNA_file is None:
-            logger.error("You must provide a rRNA file or a reference_file")
+            click.echo("You must provide a rRNA file or a reference_file", err=True)
             sys.exit(1)
 
         if options.reference_file:
-            logger.info("checking your input GFF file and rRNA feature if provided")
+            click.echo("checking your input GFF file and rRNA feature if provided")
             if options.genbank_file:
                 from sequana.genbank import GenBank
+
                 gbk = GenBank(options.genbank_file)
             if options.genbank_file is None and options.gff_file is None:
-                logger.error("Most probably you want to provide an annotation (genbank-file or gff-file)")
+                click.echo("Most probably you want to provide an annotation (genbank-file or gff-file)", err=True)
                 sys.exit(0)
 
-        # ----------------------------------------------------  others
-        cfg.input_pattern = options.input_pattern
-        cfg.input_directory = os.path.abspath(options.input_directory)
-        cfg.input_readtag = options.input_readtag
-
-        manager.exists(cfg.input_directory)
     # finalise the command and save it; copy the snakemake. update the config
     # file and save it.
     manager.teardown()
 
-    if options.run:
-        subprocess.Popen(["sh", '{}.sh'.format(NAME)], cwd=options.workdir)
 
 if __name__ == "__main__":
     main()
diff --git a/sequana_pipelines/ribofinder/ribofinder.rules b/sequana_pipelines/ribofinder/ribofinder.rules
index 8171ee6..170ba19 100644
--- a/sequana_pipelines/ribofinder/ribofinder.rules
+++ b/sequana_pipelines/ribofinder/ribofinder.rules
@@ -12,105 +12,127 @@
 #  Documentation: https://github.com/sequana/fastqc/README.rst
 ##############################################################################
 """Ribofinder pipeline"""
-import glob
-import os
 import shutil
-from os.path import join
+import os
 from collections import Counter
 
-import sequana
 
 from sequana_pipetools import PipelineManager
-from sequana_pipetools import snaketools as sm
-from sequana import logger as log
-
 from sequana.gff3 import GFF3
+from sequana import logger as log
 
 configfile: "config.yaml"
 
 manager = PipelineManager("ribofinder", config)
-manager.setup(globals(), mode="warning")
 
 
-
-__data__input = manager.getrawdata()
-
 rule pipeline:
-    input: 
+    input:
         ".sequana/rulegraph.svg",
         "outputs/proportions.png",
         "outputs/RPKM.png",
         "multiqc/multiqc_report.html"
 
-__fasta_file__ = config['general']['reference_file']
-if config['general']['genbank_file']:
-    __annot_file__   = config['general']['genbank_file']
-elif config['general']['gff_file']:
-    __annot_file__   = config['general']['gff_file']
-elif config['general']['rRNA_file']:
-    __annot_file__   = config['general']['rRNA_file']
 
-__prefix_name__ = "indexing/features"
+def get_annot_file():
+    if config['general']['genbank_file']:
+        return config['general']['genbank_file']
+    elif config['general']['gff_file']:
+        return config['general']['gff_file']
+    elif config['general']['rRNA_file']:
+        return config['general']['rRNA_file']
+        raise ValueError("You must provide a genbank of gff or file with rRNA sequences.")
+
+
+input_fasta = config['general']['reference_file']
 
 
 if manager.config.general.rRNA_file:
-    __bowtie1_index_rna__fasta = config["general"]["rRNA_file"]
-    if os.path.exists(__bowtie1_index_rna__fasta) is False:
-        log.error(f"File {__bowtie1_index_rna__fasta} does not exists. Check your config file")
+    user_file = config["general"]["rRNA_file"]
+    if os.path.exists(user_file) is False:
+        log.error(f"File {user_file} does not exists. Check your config file")
         sys.exit(1)
-elif __annot_file__.endswith(".gbk"):
+    os.makedirs("build_feature_fasta", exist_ok=True)
+    shutil.copy(user_file, "build_feature_fasta/feature.fasta")
+elif get_annot_file().endswith(".gbk"):
     # This is for genbank input
-    __build_feature_fasta__output = "build_feature_fasta/feature.fasta"
-    for this in [__fasta_file__, __annot_file__]:
+    for this in [input_fasta, get_annot_file()]:
         if os.path.exists(this) is False:
-            raise IOError("File {} not found".format(__fasta_file__))
+            raise IOError("File {} not found".format(input_fasta))
+
     rule build_feature_fasta:
         input:
-            fasta = __fasta_file__,
-            annot = __annot_file__
-        output: __build_feature_fasta__output
+            fasta = input_fasta,
+            annot = get_annot_file()
+        output: "build_feature_fasta/feature.fasta"
         run:
             from sequana.genbank import GenBank
             gg = GenBank(input.annot)
             sequence = gg.extract_fasta(input.fasta, features=['rRNA'])
             with open(output[0], "w") as fout:
                 fout.write(sequence)
-    __bowtie1_index_rna__fasta = __build_feature_fasta__output
-elif __annot_file__.endswith(".gff") or __annot_file__.endswith(".gff3"):
-    for this in [__fasta_file__, __annot_file__]:
-        if os.path.exists(this) is False:
-            raise IOError("File {} not found".format(__fasta_file__))
-    # extract rRNA feature from GFF and get corresponding fasta
-    # and gff. if no match for rRNA, save empty fasta as AAAAAAAAAAA
-    __build_feature_fasta__output = "build_feature_fasta/feature.fasta"
 
-    __extract_fasta_from_bed__input =       __fasta_file__
-    __extract_fasta_from_bed__gff =         __annot_file__
-    __extract_fasta_from_bed__feature =     config["general"]["rRNA_feature"]
-    __extract_fasta_from_bed__output =          __build_feature_fasta__output
-    __extract_fasta_from_bed__output_features = __prefix_name__ + "_rRNA.gff"
-    __extract_fasta_from_bed__log =             "indexing/get_rRNA.log"
-    # ----------------------------------------------------------------------------
-    include: sm.modules["extract_fasta_from_bed"]
-    __bowtie1_index_rna__fasta = __extract_fasta_from_bed__output
+elif get_annot_file().endswith(".gff") or get_annot_file().endswith(".gff3"):
+    for this in [input_fasta, get_annot_file()]:
+        if os.path.exists(this) is False:
+            raise IOError(f"File {this} not found")
 
 
-__bowtie1_reference__ = __bowtie1_index_rna__fasta.rsplit(".",1)[0] + "_rRNA.1.ebwt"
+    rule build_feature_fasta:
+        """ extract rRNA feature from GFF and get corresponding fasta and gff.
 
+        if there is no match for rRNA, we can use polyA AAAAAAAAAAA
+        """
+        input:
+            fasta = input_fasta,
+            gff = get_annot_file()
+        output:
+            fasta = "build_feature_fasta/feature.fasta",
+            gff = "build_feature_fasta/feature_rRNA.gff"
+        params:
+           feature = config['general']['rRNA_feature']
+        container:
+            config["apptainers"]["bedtools"]
+        shell:
+            """
+            # used to be gawk but awk is more generic and available in the container.
+            awk '{{ if ($3=="{params.feature}") print }}' {input.gff} > {output.gff}
+            if [ -s {output.gff} ]
+            then
+                bedtools getfasta -fi {input.fasta} -bed {output.gff}  -fo {output.fasta}
+            else :
+                echo -e ">empty\\nAAAAAAAAAAAAAA" > {output.fasta}
+            fi
+            """
+
+    rule samtools_faidx:
+        input:
+            fasta = "build_feature_fasta/feature.fasta"
+        output:
+            fai = "build_feature_fasta/feature.fasta.fai"
+        container:
+            config["apptainers"]["samtools"]
+        shell:
+            """
+            samtools faidx {input.fasta}
+            """
 
 
 rule bowtie1_indexing:
     input:
-        reference= __bowtie1_index_rna__fasta
+        reference= "build_feature_fasta/feature.fasta"
     output:
-        __bowtie1_reference__
+        "build_feature_fasta/feature_rRNA.1.ebwt"
     log:
         "indexing/bowtie_rRNA.log"
     params:
         options=""
-    threads: 2
+    threads:
+        2
+    container:
+        config['apptainers']['sequana_ribofinder']
     wrapper:
-        "main/wrappers/bowtie1/build"
+        f"{manager.wrappers}/wrappers/bowtie1/build"
 
 
 
@@ -126,6 +148,8 @@ rule unpigz:
     input: manager.getrawdata()
     output: temp("{sample}/unpigz/{sample}.fastq")
     threads: 4
+    container:
+        config['apptainers']['pigz']
     shell:
         """
         unpigz -p {threads} -fk --stdout {input[0]} > {output}
@@ -137,7 +161,7 @@ rule unpigz:
 rule bowtie1_mapping_rna:
     input:
         fastq="{sample}/unpigz/{sample}.fastq",
-        index=__bowtie1_reference__
+        index="build_feature_fasta/feature_rRNA.1.ebwt"
     output:
         bam="{sample}/bowtie1/{sample}.bam",
         sorted="{sample}/bowtie1/{sample}.sorted.bam"
@@ -145,9 +169,12 @@ rule bowtie1_mapping_rna:
         "{sample}/bowtie1/{sample}.log"
     params:
         options=""
-    threads: config['bowtie1_mapping_rna']['threads']
+    threads:
+        config['bowtie1_mapping_rna']['threads']
+    container:
+        config['apptainers']['sequana_ribofinder']
     wrapper:
-        "main/wrappers/bowtie1/align"
+        f"{manager.wrappers}/wrappers/bowtie1/align"
 
 
 # ======================================================== Fix bowtie log
@@ -157,7 +184,7 @@ rule fix_bowtie1_log:
     input:
         expand("{sample}/bowtie1/{sample}.log", sample=manager.samples)
     output:
-        "logs/fix_bowtie1_log"
+        "logs/fix_bowtie1_log/done"
     run:
         for filename in input:
             # we read the file
@@ -178,13 +205,13 @@ rule fix_bowtie1_log:
 rule plotting:
     input:
         bam_files=expand("{sample}/bowtie1/{sample}.sorted.bam", sample=manager.samples),
-        fasta_file=__bowtie1_index_rna__fasta
+        fasta_file= "build_feature_fasta/feature.fasta"
     output:
         png="outputs/proportions.png",
         rpkm="outputs/RPKM.png"
     run:
         import pandas as pd
-        from sequana import BAM
+        from sequana import BAM, FastA
         from pylab import tight_layout, savefig, xlabel, ylabel, clf
 
         results = []
@@ -204,7 +231,7 @@ rule plotting:
         df1 = df.copy()
         df1.columns = [x[0:30] for x in df1.columns ]
 
-        
+
         # first plot shown percentage of hits on each sequence 
         import seaborn as sns
         sns.violinplot(data=df1, orient='h')
@@ -214,7 +241,7 @@ rule plotting:
         savefig(output['png'])
 
         # now, we shown the RPKM (read count normalised by gene length)
-        from sequana import FastA
+
         f = FastA(input['fasta_file'])
         df = df.T
         L = [ f.get_lengths_as_dict()[x] for x in df.index]
@@ -235,6 +262,8 @@ rule bam_indexing:
         "{sample}/bowtie1/{sample}.sorted.bam"
     output:
         "{sample}/bowtie1/{sample}.sorted.bam.bai"
+    container:
+        config['apptainers']['sequana_ribofinder']
     shell:
         """
         bamtools index -in {input}
@@ -244,13 +273,49 @@ rule bam_indexing:
 # ========================================================== multiqc
 #
 sequana_multiqc_input = expand("{sample}/bowtie1/{sample}.sorted.bam.bai", sample=sorted(manager.samples))
-sequana_multiqc_input += ["logs/fix_bowtie1_log"]
-include: sm.modules["multiqc/2.0"]
+sequana_multiqc_input += ["logs/fix_bowtie1_log/done"]
+
+
+rule multiqc:
+    input:
+        sequana_multiqc_input
+    output:
+       "multiqc/multiqc_report.html"
+    params:
+        options=config['multiqc']['options'],
+        input_directory=config['multiqc']['input_directory'],
+        config_file=config['multiqc']['config_file'],
+        modules=config['multiqc']['modules']
+    log:
+        "multiqc/multiqc.log"
+    container:
+        config["apptainers"]["multiqc"]
+    wrapper:
+       f"{manager.wrappers}/wrappers/multiqc"
+
 
 # ========================================================== rulegraph
-#
-sequana_rulegraph_mapper = {"multiqc": "../multiqc/multiqc_report.html"}
-include: sm.modules['rulegraph']
+rule rulegraph:
+    input: str(manager.snakefile)
+    output:
+        svg = "rulegraph/rulegraph.dot"
+    params:
+        mapper = {"multiqc": "../multiqc/multiqc_report.html"},
+        configname = "config.yaml"
+    wrapper:
+        f"{manager.wrappers}/wrappers/rulegraph"
+
+
+rule dot2svg:
+    input:
+        "rulegraph/rulegraph.dot"
+    output:
+        ".sequana/rulegraph.svg"
+    container:
+        config['apptainers']['graphviz']
+    shell:
+        """dot -Tsvg {input} -o {output}"""
+
 
 
 
@@ -265,7 +330,7 @@ onsuccess:
     manager.teardown()
 
 
-    from sequana.modules_report.summary import SummaryModule2
+    from sequana.modules_report.summary import SequanaReport
     from sequana_pipelines import ribofinder
     data = {
             "name": manager.name,
@@ -297,16 +362,12 @@ onsuccess:
     except Exception:
         pass
 
-    s = SummaryModule2(data, intro=HTML)
+    data = manager.getmetadata()
+    s = SequanaReport(data, intro=HTML)
 
 
     shell("chmod -R g+w .")
     shell("rm -rf rulegraph")
 onerror:
-    print("An error occurred. See message above.")
-
-onerror:
-    from sequana_pipetools.errors import PipeError
-    p = PipeError("ribofinder")
-    p.status()
+    manager.onerror()
 
diff --git a/sequana_pipelines/ribofinder/schema.yaml b/sequana_pipelines/ribofinder/schema.yaml
index f8c1715..fb2ebb7 100644
--- a/sequana_pipelines/ribofinder/schema.yaml
+++ b/sequana_pipelines/ribofinder/schema.yaml
@@ -3,6 +3,9 @@
 
 type: map
 mapping:
+    "sequana_wrappers":
+        type: str
+        required: true
     "input_directory":
         type: str
         required: True
@@ -12,6 +15,8 @@ mapping:
     "input_pattern":
         type: str
         required: True
+    "apptainers":
+        type: any
 
     "general":
         type: map
diff --git a/sequana_pipelines/ribofinder/requirements.txt b/sequana_pipelines/ribofinder/tools.txt
similarity index 53%
rename from sequana_pipelines/ribofinder/requirements.txt
rename to sequana_pipelines/ribofinder/tools.txt
index dddf2a1..e5c02cc 100644
--- a/sequana_pipelines/ribofinder/requirements.txt
+++ b/sequana_pipelines/ribofinder/tools.txt
@@ -1,3 +1,5 @@
 bowtie
 samtools
+bedtools
+bamtools
 pigz
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 692dbab..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,13 +0,0 @@
-# a setup configuration
-[build_sphinx]
-source_dir = doc/source
-build_dir  = doc/build
-all_files  = 1
-
-
-[aliases]
-test=pytest
-
-[tool:pytest]
-# do not use --cov because it interfers with travis command
-addopts= --durations=10 --verbose  -n 1 --cov sequana_pipelines.ribofinder --cov-report term-missing
diff --git a/setup.py b/setup.py
deleted file mode 100644
index eda7af5..0000000
--- a/setup.py
+++ /dev/null
@@ -1,89 +0,0 @@
-# -*- coding: utf-8 -*-
-# License: 3-clause BSD
-from setuptools import setup, find_namespace_packages
-from setuptools.command.develop import develop
-from setuptools.command.install import install
-import subprocess
-
-_MAJOR               = 0
-_MINOR               = 11
-_MICRO               = 1
-version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
-release              = '%d.%d' % (_MAJOR, _MINOR)
-
-metainfo = {
-    'authors': {"main": ("thomas cokelaer", "thomas.cokelaer@pasteur.fr")},
-    'version': version,
-    'license' : 'new BSD',
-    'url' : "https://github.com/sequana/",
-    'description': "NGS, ribosomal, rRNA, snakemake, sequana" ,
-    'platforms' : ['Linux', 'Unix', 'MacOsX', 'Windows'],
-    'keywords' : ['NGS, ribosomal, rRNA, snakemake, sequana'],
-    'classifiers' : [
-          'Development Status :: 5 - Production/Stable',
-          'Intended Audience :: Education',
-          'Intended Audience :: End Users/Desktop',
-          'Intended Audience :: Developers',
-          'Intended Audience :: Science/Research',
-          'License :: OSI Approved :: BSD License',
-          'Operating System :: OS Independent',
-          'Programming Language :: Python :: 3.7',
-          'Programming Language :: Python :: 3.8',
-          'Programming Language :: Python :: 3.9',
-          'Topic :: Software Development :: Libraries :: Python Modules',
-          'Topic :: Scientific/Engineering :: Bio-Informatics',
-          'Topic :: Scientific/Engineering :: Information Analysis',
-          'Topic :: Scientific/Engineering :: Mathematics',
-          'Topic :: Scientific/Engineering :: Physics']
-    }
-
-NAME = "ribofinder"
-
-class Install(install):
-    def run(self):
-        cmd = "sequana_completion --name {} --force ".format(NAME)
-        try: subprocess.run(cmd.split())
-        except:pass
-        install.run(self)
-
-class Develop(develop):
-    def run(self):
-        cmd = "sequana_completion --name {} --force ".format(NAME)
-        try:subprocess.run(cmd.split())
-        except:pass
-        develop.run(self)
-
-setup(
-    name             = "sequana_{}".format(NAME),
-    version          = version,
-    maintainer       = metainfo['authors']['main'][0],
-    maintainer_email = metainfo['authors']['main'][1],
-    author           = metainfo['authors']['main'][0],
-    author_email     = metainfo['authors']['main'][1],
-    long_description = open("README.rst").read(),
-    keywords         = metainfo['keywords'],
-    description      = metainfo['description'],
-    license          = metainfo['license'],
-    platforms        = metainfo['platforms'],
-    url              = metainfo['url'],
-    classifiers      = metainfo['classifiers'],
-
-    # package installation
-    packages = ["sequana_pipelines.ribofinder"],
-
-    install_requires = open("requirements.txt").read(),
-
-    # This is recursive include of data files
-    exclude_package_data = {"": ["__pycache__"]},
-    package_data = {
-        '': ['*.yaml', "*.rules", "*.json", "requirements.txt", "*png"],
-        'sequana_pipelines.ribofinder.data' : ['*.*'], 
-        },
-
-    zip_safe=False,
-
-    entry_points = {'console_scripts':[
-        'sequana_ribofinder=sequana_pipelines.ribofinder.main:main']
-    }
-
-)
diff --git a/test/test_main.py b/test/test_main.py
index 87f2dc2..091b00c 100644
--- a/test/test_main.py
+++ b/test/test_main.py
@@ -3,6 +3,9 @@
 import tempfile
 import subprocess
 import sys
+from click.testing import CliRunner
+from sequana_pipelines.ribofinder.main import main
+
 
 from . import test_dir
 
@@ -17,10 +20,12 @@ def test_standalone_subprocess():
 
 def test_standalone_script():
     directory = tempfile.TemporaryDirectory()
-    import sequana_pipelines.ribofinder.main as m
-    sys.argv = ["test", "--input-directory", sharedir, 
-            "--working-directory", directory.name, "--force", "--rRNA-file", sharedir+"feature.fasta"]
-    m.main()
+
+
+    runner = CliRunner()
+    results = runner.invoke(main, [ "--input-directory", sharedir, 
+            "--working-directory", directory.name, "--force", "--rRNA-file", sharedir+"feature.fasta"])
+    assert results.exit_code == 0
 
 
 def test_full_rRNA_file():
@@ -29,7 +34,7 @@ def test_full_rRNA_file():
         cmd = f"sequana_ribofinder --input-directory {sharedir} "
         cmd += f"--working-directory {wk}  --force --rRNA-file {sharedir}/feature.fasta"
         subprocess.call(cmd.split())
-        stat = subprocess.call("sh ribofinder.sh".split(), cwd=wk)
+        stat = subprocess.call("bash ribofinder.sh".split(), cwd=wk)
         assert os.path.exists(wk + "/summary.html")
 
 def test_full_rRNA_extract():
@@ -38,7 +43,7 @@ def test_full_rRNA_extract():
         cmd = f"sequana_ribofinder --input-directory {sharedir} "
         cmd += f"--working-directory {wk}  --force --reference-file {sharedir}/Lepto.fa --gff-file {sharedir}/Lepto.gff"
         subprocess.call(cmd.split())
-        stat = subprocess.call("sh ribofinder.sh".split(), cwd=wk)
+        stat = subprocess.call("bash ribofinder.sh".split(), cwd=wk)
         assert os.path.exists(wk + "/summary.html")
 
 def test_version():