diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
deleted file mode 100644
index 33ad34d..0000000
--- a/.github/workflows/awsfulltest.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
-# It can be additionally triggered manually with GitHub actions workflow dispatch button.
-# It runs the -profile 'test_full' on AWS batch
-
-on:
-  release:
-    types: [published]
-  workflow_dispatch:
-jobs:
-  run-tower:
-    name: Run AWS full tests
-    if: github.repository == 'socialgene/sgnf'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
-        with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/socialgene/sgnf/work-${{ github.sha }}
-          parameters: |
-            {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/socialgene/sgnf/results-${{ github.sha }}"
-            }
-          profiles: test_full
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: Tower debug log file
-          path: |
-            tower_action_*.log
-            tower_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
deleted file mode 100644
index 0c7cecf..0000000
--- a/.github/workflows/awstest.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: nf-core AWS test
-# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
-# It runs the -profile 'test' on AWS batch
-
-on:
-  workflow_dispatch:
-jobs:
-  run-tower:
-    name: Run AWS tests
-    if: github.repository == 'socialgene/sgnf'
-    runs-on: ubuntu-latest
-    steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
-        with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/socialgene/sgnf/work-${{ github.sha }}
-          parameters: |
-            {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/socialgene/sgnf/results-test-${{ github.sha }}"
-            }
-          profiles: test
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: Tower debug log file
-          path: |
-            tower_action_*.log
-            tower_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2d83fd2..8d5d7a9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index b2a2941..56e65c4 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -17,9 +17,9 @@ jobs:
         env: [["sgpy-base", "dockerfiles/sgpy/sgpy_base"]]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Log in to Docker Hub
         uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
         with:
@@ -73,9 +73,9 @@ jobs:
           ]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Log in to Docker Hub
         uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
         with:
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index c024629..e316594 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,7 +14,7 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-node@v3
 
@@ -27,7 +27,7 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-node@v3
 
@@ -41,7 +41,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: black
         uses: psf/black@stable
 
@@ -49,7 +49,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
@@ -77,7 +77,7 @@ jobs:
 
 # - name: Upload linting log file artifact
 #   if: ${{ always() }}
-#   uses: actions/upload-artifact@v3
+#   uses: actions/upload-artifact@v4
 #   with:
 #     name: linting-logs
 #     path: |
diff --git a/dockerfiles/hmmer/Dockerfile b/dockerfiles/hmmer/Dockerfile
index 47d0aa5..8a6c9cf 100644
--- a/dockerfiles/hmmer/Dockerfile
+++ b/dockerfiles/hmmer/Dockerfile
@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.1.0
+FROM mambaorg/micromamba:1.5.0
 
 COPY environment.yaml /tmp/env.yaml
 
diff --git a/dockerfiles/hmmer_plus/Dockerfile b/dockerfiles/hmmer_plus/Dockerfile
index 47d0aa5..8a6c9cf 100644
--- a/dockerfiles/hmmer_plus/Dockerfile
+++ b/dockerfiles/hmmer_plus/Dockerfile
@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.1.0
+FROM mambaorg/micromamba:1.5.0
 
 COPY environment.yaml /tmp/env.yaml
 
diff --git a/dockerfiles/minimal/Dockerfile b/dockerfiles/minimal/Dockerfile
index 47d0aa5..8a6c9cf 100644
--- a/dockerfiles/minimal/Dockerfile
+++ b/dockerfiles/minimal/Dockerfile
@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.1.0
+FROM mambaorg/micromamba:1.5.0
 
 COPY environment.yaml /tmp/env.yaml
 
diff --git a/dockerfiles/sgpy/sgpy_base/Dockerfile b/dockerfiles/sgpy/sgpy_base/Dockerfile
index 9712e36..51bb1c6 100644
--- a/dockerfiles/sgpy/sgpy_base/Dockerfile
+++ b/dockerfiles/sgpy/sgpy_base/Dockerfile
@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.1.0
+FROM mambaorg/micromamba:1.5.0
 
 COPY environment.yaml /tmp/env.yaml
 
@@ -7,7 +7,7 @@ RUN micromamba install -y -n base -f /tmp/env.yaml && \
 
 ### Add Neo4j, remove then re-add the needed directories/files to avoid any potential permission issues
 # https://neo4j.com/docs/operations-manual/current/configuration/file-locations/
-RUN /opt/conda/bin/wget -q https://neo4j.com/artifact.php?name=neo4j-community-5.7.0-unix.tar.gz -O neo4j.tar.gz \
+RUN /opt/conda/bin/wget -q https://neo4j.com/artifact.php?name=neo4j-community-5.16.0-unix.tar.gz -O neo4j.tar.gz \
     && tar -xf neo4j.tar.gz \
     && rm neo4j.tar.gz \
     && mv neo4j* neo4j \