diff --git a/.github/workflows/deploy-docker.yaml b/.github/workflows/deploy-docker.yaml
index 35a395f8..cc0a6953 100644
--- a/.github/workflows/deploy-docker.yaml
+++ b/.github/workflows/deploy-docker.yaml
@@ -51,7 +51,7 @@ jobs:
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           push: ${{ contains(github.ref, 'master') || startsWith(github.ref, 'refs/tags') }}
           tags: ${{ steps.meta.outputs.tags }}
diff --git a/.github/workflows/mega-linter.yml b/.github/workflows/mega-linter.yml
index 7d976cce..d4bb6c94 100644
--- a/.github/workflows/mega-linter.yml
+++ b/.github/workflows/mega-linter.yml
@@ -27,7 +27,7 @@ jobs:
     steps:
       # Git Checkout
       - name: Checkout Code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           token: ${{ secrets.PAT || secrets.GITHUB_TOKEN }}
           fetch-depth: 0
@@ -37,7 +37,7 @@ jobs:
         id: ml
         # You can override Mega-Linter flavor used to have faster performances
         # More info at https://megalinter.github.io/flavors/
-        uses: megalinter/megalinter@v6
+        uses: megalinter/megalinter@v8
         env:
           # All available variables are described in documentation
           # https://megalinter.github.io/configuration/
@@ -48,12 +48,11 @@ jobs:
       # Upload Mega-Linter artifacts
       - name: Archive production artifacts
         if: ${{ success() }} || ${{ failure() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Mega-Linter reports
           path: |
-            report
-            mega-linter.log
+            megalinter-reports
 
       # Create pull request if applicable (for now works only on PR from same repository, not from forks)
       - name: Create Pull Request with applied fixes
diff --git a/.github/workflows/run_regression_tests.yaml b/.github/workflows/run_regression_tests.yaml
index ca790bf6..49ecfc41 100644
--- a/.github/workflows/run_regression_tests.yaml
+++ b/.github/workflows/run_regression_tests.yaml
@@ -18,15 +18,15 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
             lfs: false
 
       - name: Install conda environment dependencies
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge
           python-version: "3.11"
           mamba-version: "*"
           channels: conda-forge,bioconda #,defaults # see: https://github.com/conda-forge/status/issues/144
@@ -75,16 +75,16 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
             lfs: false
             # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS
 
       - name: Install conda environment dependencies
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge
           python-version: ${{ matrix.python-version }}
           mamba-version: "*"
           channels: conda-forge,bioconda #,defaults # see: https://github.com/conda-forge/status/issues/144
@@ -104,9 +104,12 @@ jobs:
         run: ./regression_tests.sh ${{ matrix.virus }}
 
       - name: Archive code coverage results
-        uses: actions/upload-artifact@v3
+        if: ${{ success() }} || ${{ failure() }}
+        uses: actions/upload-artifact@v4
         with:
-          name: regression test output and diffs
+          name: regression_test_${{ matrix.os }}_${{ matrix.python-version }}_${{ matrix.virus }}
           path: |
             /tmp/v-pipe_tests/*
+            !/tmp/v-pipe_tests/.snakemake/conda/*/
+          include-hidden-files: true
           if-no-files-found: ignore
diff --git a/.github/workflows/snakedeploy_tests.yaml b/.github/workflows/snakedeploy_tests.yaml
index b5e82ff0..76931a06 100644
--- a/.github/workflows/snakedeploy_tests.yaml
+++ b/.github/workflows/snakedeploy_tests.yaml
@@ -27,7 +27,7 @@ jobs:
 
     steps:
       - name: Checkout test data
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
             sparse-checkout: |
                 tests
@@ -37,10 +37,10 @@ jobs:
             # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS
 
       - name: Install conda environment dependencies
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge
           python-version: "3.11" # temporary fix for snakemake issue #2480
           mamba-version: "*"
           channels: conda-forge,bioconda
@@ -81,11 +81,13 @@ jobs:
                 --keep-going
 
       - name: Archive test results
-        uses: actions/upload-artifact@v3
+        if: ${{ success() }} || ${{ failure() }}
+        uses: actions/upload-artifact@v4
         with:
-          name: test_output
+          name: test_output_${{ matrix.virus }}
           path: |
             ./*
             !./.git
             !./.snakemake/conda/*/
+          include-hidden-files: true
           if-no-files-found: ignore
diff --git a/.github/workflows/test-docker.yaml b/.github/workflows/test-docker.yaml
index 2a91b52e..59568c60 100644
--- a/.github/workflows/test-docker.yaml
+++ b/.github/workflows/test-docker.yaml
@@ -42,7 +42,7 @@ jobs:
 
       - name: Build and save
         id: docker_build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           push: false
           tags: ${{ steps.meta.outputs.tags }}
@@ -50,7 +50,7 @@ jobs:
           outputs: type=docker,dest=./vpipe-docker.tar.zst,compression=zstd,compression-level=6
 
       - name: Upload artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: "( !contains(github.ref, 'master') && !startsWith(github.ref, 'refs/tags') )"
         with:
           name: vpipe-docker
diff --git a/.github/workflows/tutorials.yaml b/.github/workflows/tutorials.yaml
index 6f5e10b6..5feb1c11 100644
--- a/.github/workflows/tutorials.yaml
+++ b/.github/workflows/tutorials.yaml
@@ -24,7 +24,7 @@ jobs:
         run: rm -rf /opt/hostedtoolcache
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
             sparse-checkout: |
                 docs
@@ -33,10 +33,10 @@ jobs:
             lfs: false
 
       - name: Install conda environment dependencies
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge
           mamba-version: "*"
           channels: conda-forge,bioconda
           channel-priority: strict
@@ -57,16 +57,16 @@ jobs:
         run: tar --zstd -cvf vpipeinstallation.tar.zst ./docs/vp-analysis
 
       - name: Keep installation
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: VPipeInstallation
           path: vpipeinstallation.tar.zst
           if-no-files-found: error
 
       - name: Save notebooks
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: JupyterNotebooks
+          name: JupyterNotebooks-Install
           path: ./docs/*.ipynb
 
 
@@ -93,7 +93,7 @@ jobs:
         run: rm -rf /opt/hostedtoolcache
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
             sparse-checkout: |
                 docs
@@ -102,7 +102,7 @@ jobs:
             lfs: false
 
       - name: Reuse installation
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
             name: VPipeInstallation
 
@@ -110,10 +110,10 @@ jobs:
         run: tar --zstd -xvf vpipeinstallation.tar.zst
 
       - name: Install conda environment dependencies
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge
           python-version: "3.11"
           mamba-version: "*"
           channels: conda-forge,bioconda
@@ -131,9 +131,9 @@ jobs:
         run: ./convert.sh --branch tutorial*_${{ matrix.virus }}.md
 
       - name: Save notebooks
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: JupyterNotebooks
+          name: JupyterNotebooks-${{ matrix.virus }}
           path: ./docs/*.ipynb
 
       # - name: Publish