Bump dependency versions (#92)

* build(deps): bump actions/checkout from v3 to v4

* refactor: remove unused nf-core GH actions

* build(deps): bump micromamba docker from 1.1.0 to 1.5.0

* build(deps): bump Neo4j from 5.7.0 to 5.16.0

.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

.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:

.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
 
@@ -41,15 +41,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: black
         uses: psf/black@stable
 
   nf-core:
     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: |

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
 

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
 

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
 

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 \