Merge pull request #42 from Ferlab-Ste-Justine/feat/CLIN-3614-add-doc…

…ker-image-for-exomiser-v13.1 feat: CLIN-3614 add docker image for exomiser 13.1.0
Ferlab-Ste-Justine · Dec 5, 2024 · 56cb96b · 56cb96b
2 parents c43ca3d + aee2b99
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diff --git a/.github/workflows/publish_with_latest.yml b/.github/workflows/publish_with_latest.yml
@@ -21,16 +21,30 @@ jobs:
           dockerfile: containers/nextflow/Dockerfile
           tag_format: "latest"
   push-exomiser:
-      name: Publish Exomiser Image using latest tags
-      runs-on: ubuntu-latest
-      steps:
-        - uses: actions/checkout@v3
-        - name: Push the image on the registry
-          uses: Ferlab-Ste-Justine/action-push-image@v2
-          with:
-            username: ${{ secrets.FERLAB_DOCKER_HUB_USER }}
-            password: ${{ secrets.FERLAB_DOCKER_HUB_TOKEN }}
-            image: ferlabcrsj/exomiser
-            location: containers/exomiser
-            dockerfile: containers/exomiser/Dockerfile
-            tag_format: "latest"
+    name: Publish Exomiser Image using latest tags
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Push the image on the registry
+        uses: Ferlab-Ste-Justine/action-push-image@v2
+        with:
+          username: ${{ secrets.FERLAB_DOCKER_HUB_USER }}
+          password: ${{ secrets.FERLAB_DOCKER_HUB_TOKEN }}
+          image: ferlabcrsj/exomiser
+          location: containers/exomiser
+          dockerfile: containers/exomiser/Dockerfile
+          tag_format: "latest"
+  push-exomiser-13:
+    name: Publish Exomiser 13.1.0 Image using latest tags
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Push the image on the registry
+        uses: Ferlab-Ste-Justine/action-push-image@v2
+        with:
+          username: ${{ secrets.FERLAB_DOCKER_HUB_USER }}
+          password: ${{ secrets.FERLAB_DOCKER_HUB_TOKEN }}
+          image: ferlabcrsj/exomiser
+          location: containers/exomiser-13
+          dockerfile: containers/exomiser-13/Dockerfile
+          tag_format: "13.1.0-latest"
diff --git a/.github/workflows/publish_with_semver_tag.yml b/.github/workflows/publish_with_semver_tag.yml
@@ -33,4 +33,18 @@ jobs:
             image: ferlabcrsj/exomiser
             location: containers/exomiser
             dockerfile: containers/exomiser/Dockerfile
-            tag_format: "{semver}"
+            tag_format: "{semver}"
+  push-exomiser-13:
+        name: Publish Exomiser 13.1.0 Image using tags
+        runs-on: ubuntu-latest
+        steps:
+          - uses: actions/checkout@v3
+          - name: Push the image on the registry
+            uses: Ferlab-Ste-Justine/action-push-image@v2
+            with:
+              username: ${{ secrets.FERLAB_DOCKER_HUB_USER }}
+              password: ${{ secrets.FERLAB_DOCKER_HUB_TOKEN }}
+              image: ferlabcrsj/exomiser
+              location: containers/exomiser-13
+              dockerfile: containers/exomiser-13/Dockerfile
+              tag_format: "13.1.0-{semver}"
diff --git a/.github/workflows/publish_with_sha.yml b/.github/workflows/publish_with_sha.yml
@@ -21,16 +21,30 @@ jobs:
           dockerfile: containers/nextflow/Dockerfile
           tag_format: "{sha}-{timestamp}"
   push-exomiser:
-      name: Publish Exomiser Image using commit sha and timestamp
-      runs-on: ubuntu-latest
-      steps:
-        - uses: actions/checkout@v3
-        - name: Push the image on the registry
-          uses: Ferlab-Ste-Justine/action-push-image@v2
-          with:
-            username: ${{ secrets.FERLAB_DOCKER_HUB_USER }}
-            password: ${{ secrets.FERLAB_DOCKER_HUB_TOKEN }}
-            image: ferlabcrsj/exomiser
-            location: containers/exomiser
-            dockerfile: containers/exomiser/Dockerfile
-            tag_format: "{sha}-{timestamp}"
+    name: Publish Exomiser Image using commit sha and timestamp
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Push the image on the registry
+        uses: Ferlab-Ste-Justine/action-push-image@v2
+        with:
+          username: ${{ secrets.FERLAB_DOCKER_HUB_USER }}
+          password: ${{ secrets.FERLAB_DOCKER_HUB_TOKEN }}
+          image: ferlabcrsj/exomiser
+          location: containers/exomiser
+          dockerfile: containers/exomiser/Dockerfile
+          tag_format: "{sha}-{timestamp}"
+  push-exomiser-13:
+    name: Publish Exomiser 13.1.0 Image using commit sha and timestamp
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Push the image on the registry
+        uses: Ferlab-Ste-Justine/action-push-image@v2
+        with:
+          username: ${{ secrets.FERLAB_DOCKER_HUB_USER }}
+          password: ${{ secrets.FERLAB_DOCKER_HUB_TOKEN }}
+          image: ferlabcrsj/exomiser
+          location: containers/exomiser-13
+          dockerfile: containers/exomiser-13/Dockerfile
+          tag_format: "13.1.0-{sha}-{timestamp}"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,14 +10,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#41](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/41) Allow to customize the vep command
 - [#41](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/41) Improve parameter schema for params max_disk, max_memory, max_time
 - [#41](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/41) Consider only stable nextflow versions for ci test
+- [#42](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/42) Add docker image for exomiser 13.1.0
 
 ### `Known issues`
 - The nf-core modules that we are using have a potential performance flaw. Typically, the regex used to describe the output files also match the input files (ex: "*.vcf"), which can cause unnecessary file transfers.  This has already proven to cause issues on fusion. One fix could be to transfer the whole modules to local to perform the small change necessary to fix this.
 - The VEP cache version used in the CQDG environment (112) does not match the default configured VEP version (111). This issue can be avoided by overriding the Docker container of the ensemblevep process. If no project is using VEP version 111, it should not be used as the default value.
 
 
 ### `Fixed`
-- [#51](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/41) Fix vep url pointing to the wrong vep version in the reference data documentation.
+- [#41](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/41) Fix vep url pointing to the wrong vep version in the reference data documentation.
 
 ## v2.1.0dev
 

diff --git a/containers/README.md b/containers/README.md
@@ -6,7 +6,14 @@ utilities such as the AWS CLI and Rclone. Additionally, it provides more basic l
 not included in the base nextflow image.
 
 ### Exomiser
-This Docker image is based on the official Exomiser Docker image. It includes Exomiser tools but modifies the entrypoint to work with Nextflow on Kubernetes.
+
+This Docker image is based on the official exomiser Docker image exomiser exomiser-cli:14.0.0-bash. 
+It is modified for compatibility with nextflow.
+
+### Exomiser-13
+
+This is a docker image allowing to run exomiser 13.1.0. One can substitute the resulting image with our default
+exomiser image to run the pipeline with exomser 13.1.0.
 
 ## Local Testing Commands
 Here is an example for the Nextflow image. You can adapt these commands for other images as needed.

diff --git a/containers/exomiser-13/Dockerfile b/containers/exomiser-13/Dockerfile
@@ -0,0 +1,42 @@
+ARG EXOMISER_VERSION=13.1.0
+
+# -------------------------------------------------------------------------- #
+# Stage 1: using the distroless image to obtain exomiser distribution files  #
+#                                                                            #
+# We are using this image to guarantee the same packaging strategy as        #
+# in other exomiser-cli images                                               #
+# -------------------------------------------------------------------------- #
+FROM exomiser/exomiser-cli:${EXOMISER_VERSION} AS builder
+
+
+# -------------------------------------------------------------- #
+# Stage 2: Create an image similar to exomiser cli bash images   #
+#                                                                #
+# We replicate only the necessary logic to launch the same java  #
+# command as in other Exomiser images.                           #
+# -------------------------------------------------------------- #
+
+FROM eclipse-temurin:17.0.6_10-jre AS exomiser-cli-bash
+
+COPY --from=builder /app /app
+
+
+# ---------------------------------- #
+# Stage 3: Add nextflow requirements #
+# ---------------------------------- #
+
+FROM exomiser-cli-bash
+
+ARG EXOMISER_VERSION
+
+# Adding ps to the container (required by nextflow)
+RUN apt-get update && \
+    apt-get install -y procps=2:3.3.17-6ubuntu2.1 && \
+    rm -rf /var/lib/apt/lists/*
+
+
+# Create a file containing the exomiser version, as there is no way to retrieve it from the exomiser-cli.
+RUN echo ${EXOMISER_VERSION} > EXOMISER_VERSION.txt
+
+# Required to execute exomiser docker with nextflow
+ENTRYPOINT [  ]