diff --git a/.github/workflows/advanced.yaml b/.github/workflows/advanced.yaml
new file mode 100644
index 00000000..decbe086
--- /dev/null
+++ b/.github/workflows/advanced.yaml
@@ -0,0 +1,185 @@
+name: MosaiCatcher advanced modules checks
+
+on:
+  workflow_dispatch:
+    inputs:
+      logLevel:
+        description: "Log level"
+        required: true
+        default: "warning"
+        type: choice
+        options:
+          - info
+          - warning
+          - debug
+  schedule:
+    - cron: "0 0 * * 0"
+
+jobs:
+  Testing-with-MultiQC:
+    runs-on: ubuntu-latest
+    needs:
+      - Formatting
+      - Linting
+      - Testing-basic-v7
+      - Testing-basic-with-ashleys
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          # lfs: true
+
+      - name: Git Submodule Update
+        run: |
+          git pull --recurse-submodules
+          git submodule update --remote --recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Add Conda to system path
+        run: echo "$CONDA/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: conda install -c conda-forge mamba
+
+      - name: Setup Snakemake
+        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
+
+      - name: List options of workflow
+        run: |
+          snakemake --cores 1 --config list_commands=True --verbose --debug
+
+      - name: Run workflow
+        run: |
+          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config MultiQC=True ashleys_pipeline=True \
+          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
+
+  Testing-with-ms-norm:
+    runs-on: ubuntu-latest
+    needs:
+      - Formatting
+      - Linting
+      - Testing-basic-v7
+      - Testing-basic-with-ashleys
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          # lfs: true
+
+      - name: Git Submodule Update
+        run: |
+          git pull --recurse-submodules
+          git submodule update --remote --recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Add Conda to system path
+        run: echo "$CONDA/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: conda install -c conda-forge mamba
+
+      - name: Setup Snakemake
+        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
+
+      - name: List options of workflow
+        run: |
+          snakemake --cores 1 --config list_commands=True --verbose --debug
+
+      - name: Run workflow
+        run: |
+          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config multistep_normalisation=True ashleys_pipeline=True \
+          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
+
+  Testing-with-breakpointR-only:
+    runs-on: ubuntu-latest
+    needs:
+      - Formatting
+      - Linting
+      - Testing-basic-v7
+      - Testing-basic-with-ashleys
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          # lfs: true
+
+      - name: Git Submodule Update
+        run: |
+          git pull --recurse-submodules
+          git submodule update --remote --recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Add Conda to system path
+        run: echo "$CONDA/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: conda install -c conda-forge mamba
+
+      - name: Setup Snakemake
+        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
+
+      - name: List options of workflow
+        run: |
+          snakemake --cores 1 --config list_commands=True --verbose --debug
+
+      - name: Run workflow
+        run: |
+          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config breakpointR=True breakpointR_only=True \
+          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
+
+  Testing-with-whatshap-only:
+    runs-on: ubuntu-latest
+    needs:
+      - Formatting
+      - Linting
+      - Testing-basic-v7
+      - Testing-basic-with-ashleys
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          # lfs: true
+
+      - name: Git Submodule Update
+        run: |
+          git pull --recurse-submodules
+          git submodule update --remote --recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Add Conda to system path
+        run: echo "$CONDA/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: conda install -c conda-forge mamba
+
+      - name: Setup Snakemake
+        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
+
+      - name: List options of workflow
+        run: |
+          snakemake --cores 1 --config list_commands=True --verbose --debug
+
+      - name: Run workflow
+        run: |
+          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config whatshap_only=True \
+          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
diff --git a/.github/workflows/assemblies.yaml b/.github/workflows/assemblies.yaml
index 0f142752..2195ae16 100644
--- a/.github/workflows/assemblies.yaml
+++ b/.github/workflows/assemblies.yaml
@@ -1,9 +1,17 @@
 name: MosaiCatcher assemblies checks
 
 on:
-  push:
-    branches:
-      - "**"
+  workflow_dispatch:
+    inputs:
+      logLevel:
+        description: "Log level"
+        required: true
+        default: "warning"
+        type: choice
+        options:
+          - info
+          - warning
+          - debug
   schedule:
     - cron: "0 0 * * 0"
 
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 3d0d546c..3bb74370 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -24,7 +24,7 @@ jobs:
   Linting:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout repository with submodules
+      - name: Checkout repository without submodules
         uses: actions/checkout@v4
         # with:
         #   submodules: "recursive" # Ensures all submodules are checked out
@@ -65,14 +65,10 @@ jobs:
     #   - Formatting
     #   - Linting
     steps:
-      - name: Checkout repository with submodules and LFS
+      - name: Checkout repository with submodules
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          # lfs: true
-
-      # - name: Pull LFS objects in submodules
-      #   run: git submodule foreach --recursive 'git pull origin main'
 
       # Update references
       - name: Git Submodule Update
@@ -121,7 +117,7 @@ jobs:
     #   - Formatting
     #   - Linting
     steps:
-      - name: Checkout repository with submodules and LFS
+      - name: Checkout repository with submodules
         uses: actions/checkout@v4
         with:
           submodules: recursive
@@ -166,171 +162,3 @@ jobs:
         run: |
           snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config ashleys_pipeline=True \
           --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
-
-  Testing-with-MultiQC:
-    runs-on: ubuntu-latest
-    needs:
-      - Formatting
-      - Linting
-      - Testing-basic-v7
-      - Testing-basic-with-ashleys
-    steps:
-      - name: Checkout repository with submodules and LFS
-        uses: actions/checkout@v4
-        with:
-          submodules: recursive
-          # lfs: true
-
-      - name: Git Submodule Update
-        run: |
-          git pull --recurse-submodules
-          git submodule update --remote --recursive
-
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-
-      - name: Add Conda to system path
-        run: echo "$CONDA/bin" >> $GITHUB_PATH
-
-      - name: Install dependencies
-        run: conda install -c conda-forge mamba
-
-      - name: Setup Snakemake
-        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
-
-      - name: List options of workflow
-        run: |
-          snakemake --cores 1 --config list_commands=True --verbose --debug
-
-      - name: Run workflow
-        run: |
-          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config MultiQC=True ashleys_pipeline=True \
-          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
-
-  Testing-with-ms-norm:
-    runs-on: ubuntu-latest
-    needs:
-      - Formatting
-      - Linting
-      - Testing-basic-v7
-      - Testing-basic-with-ashleys
-    steps:
-      - name: Checkout repository with submodules and LFS
-        uses: actions/checkout@v4
-        with:
-          submodules: recursive
-          # lfs: true
-
-      - name: Git Submodule Update
-        run: |
-          git pull --recurse-submodules
-          git submodule update --remote --recursive
-
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-
-      - name: Add Conda to system path
-        run: echo "$CONDA/bin" >> $GITHUB_PATH
-
-      - name: Install dependencies
-        run: conda install -c conda-forge mamba
-
-      - name: Setup Snakemake
-        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
-
-      - name: List options of workflow
-        run: |
-          snakemake --cores 1 --config list_commands=True --verbose --debug
-
-      - name: Run workflow
-        run: |
-          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config multistep_normalisation=True ashleys_pipeline=True \
-          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
-
-  Testing-with-breakpointR-only:
-    runs-on: ubuntu-latest
-    needs:
-      - Formatting
-      - Linting
-      - Testing-basic-v7
-      - Testing-basic-with-ashleys
-    steps:
-      - name: Checkout repository with submodules and LFS
-        uses: actions/checkout@v4
-        with:
-          submodules: recursive
-          # lfs: true
-
-      - name: Git Submodule Update
-        run: |
-          git pull --recurse-submodules
-          git submodule update --remote --recursive
-
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-
-      - name: Add Conda to system path
-        run: echo "$CONDA/bin" >> $GITHUB_PATH
-
-      - name: Install dependencies
-        run: conda install -c conda-forge mamba
-
-      - name: Setup Snakemake
-        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
-
-      - name: List options of workflow
-        run: |
-          snakemake --cores 1 --config list_commands=True --verbose --debug
-
-      - name: Run workflow
-        run: |
-          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config breakpointR=True breakpointR_only=True \
-          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
-
-  Testing-with-whatshap-only:
-    runs-on: ubuntu-latest
-    needs:
-      - Formatting
-      - Linting
-      - Testing-basic-v7
-      - Testing-basic-with-ashleys
-    steps:
-      - name: Checkout repository with submodules and LFS
-        uses: actions/checkout@v4
-        with:
-          submodules: recursive
-          # lfs: true
-
-      - name: Git Submodule Update
-        run: |
-          git pull --recurse-submodules
-          git submodule update --remote --recursive
-
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-
-      - name: Add Conda to system path
-        run: echo "$CONDA/bin" >> $GITHUB_PATH
-
-      - name: Install dependencies
-        run: conda install -c conda-forge mamba
-
-      - name: Setup Snakemake
-        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
-
-      - name: List options of workflow
-        run: |
-          snakemake --cores 1 --config list_commands=True --verbose --debug
-
-      - name: Run workflow
-        run: |
-          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config whatshap_only=True \
-          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
diff --git a/.github/workflows/release_please.yaml b/.github/workflows/release_please.yaml
index 4339008c..bfd0e4d1 100644
--- a/.github/workflows/release_please.yaml
+++ b/.github/workflows/release_please.yaml
@@ -1,15 +1,17 @@
 name: "Create tag & release"
 
-# on:
-#   push:
-#     branches:
-#       - master
-
 on:
-  pull_request:
-    types: [closed]
-    branches:
-      - master
+  workflow_dispatch:
+    inputs:
+      logLevel:
+        description: "Log level"
+        required: true
+        default: "warning"
+        type: choice
+        options:
+          - info
+          - warning
+          - debug
 
 jobs:
   tagged-release:
diff --git a/config/config.yaml b/config/config.yaml
index 846efcac..7ee98478 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -3,10 +3,10 @@
 # --------------------------------------------------------
 
 # MosaiCatcher version
-version: 2.3.2
+version: 2.3.3
 
 # Ashleys-QC pipeline version
-ashleys_pipeline_version: 2.3.2
+ashleys_pipeline_version: 2.3.3
 
 # Email for notifications about the pipeline's status
 email: ""
@@ -46,6 +46,7 @@ MultiQC: False
 # Enable or disable ashleys-qc automatic classification
 bypass_ashleys: False
 
+# Whether to use paired-end data or not
 paired_end: True
 
 # --------------------------------------------------------
diff --git a/config/config_metadata.yaml b/config/config_metadata.yaml
index 4cf2e5b9..87fee593 100644
--- a/config/config_metadata.yaml
+++ b/config/config_metadata.yaml
@@ -22,6 +22,13 @@ MultiQC:
   required: False
   default: False
   category: "Quality Control"
+paired_end:
+  desc: "Enable / Disable paired-end data"
+  type: bool
+  required: False
+  default: True
+  lint_check: True
+  category: "Quality Control"
 multistep_normalisation:
   desc: "Enable / Disable multistep normalisation"
   type: bool
diff --git a/workflow/Snakefile b/workflow/Snakefile
index fb019a0c..38093a48 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -23,8 +23,8 @@ if config["ashleys_pipeline"] is True:
             github(
                 "friendsofstrandseq/ashleys-qc-pipeline",
                 path="workflow/Snakefile",
-                # tag=str(config["ashleys_pipeline_version"]),
-                branch="dev",
+                tag=str(config["ashleys_pipeline_version"]),
+                # branch="dev",
             )
         config:
             config