.github/workflows/ci.yml

-Original file line number
+Diff line change
@@ -0,0 +1,62 @@
+    # This is a basic workflow to help you get started with Actions
+    name: CI
+    # Controls when the action will run.
+    # Triggers the workflow on push or pull request events
+    on: [push, pull_request, workflow_dispatch]
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: true
+    # A workflow run is made up of one or more jobs that can run sequentially or in parallel
+    jobs:
+      # This workflow contains a second job called "build2"
+      test_MobiCT:
+        # avoid to run twice push and PR
+        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+        # The type of runner that the job will run on
+        runs-on: ubuntu-24.04
+        services:
+          docker:
+            image: docker:dind
+            options: --privileged --shm-size=2g
+            volumes:
+              - /var/run/docker.sock:/var/run/docker.sock:ro
+        # Steps represent a sequence of tasks that will be executed as part of the job
+        steps:
+          # Install/cache OpenJDK
+          - name: Cache OpenJDK
+            id: cache-openjdk
+            uses: actions/cache@v3
+            with:
+              path: /usr/lib/jvm/java-11-openjdk-amd64
+              key: ${{ runner.os }}-openjdk-11
+              restore-keys: |
+                ${{ runner.os }}-openjdk-11
+          - name: Install openjdk
+            if: ${{ steps.cache-openjdk.outputs.cache-hit != 'true' }}
+            run: sudo apt-get install openjdk-11-jdk
+          # Install/cache nextflow
+          - name: Cache nextflow
+            id: cache-nextflow
+            uses: actions/cache@v3
+            with:
+              path: /usr/local/bin/nextflow
+              key: ${{ runner.os }}-nextflow
+              restore-keys: |
+                ${{ runner.os }}-nextflow
+          - name: Install Nextflox
+            if: ${{ steps.cache-nextflow.outputs.cache-hit != 'true' }}
+            run: curl -s https://get.nextflow.io | bash && mv nextflow /usr/local/bin && chmod +x /usr/local/bin/nextflow
+          # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+          - uses: actions/checkout@v3
+          # Run tests sequentialy
+          - name: test
+            run: nextflow run -ansi-log -profile docker,test,ci MobiCT.nf

Example_data/panel_lung.bed

-Original file line number
+Diff line change
@@ -1,8 +1,5 @@
-    chr12	25245268	25245388	NM_033360	1
-    chr15	90088586	90088747	NM_002168	1
-    chr2	208248368	208248660	NM_005896	1
-    chr7	55173921	55174041	NM_005228	1
-    chr7	55174711	55174831	NM_005228	1
-    chr7	55181292	55181478	NM_005228	1
-    chr7	55191718	55191874	NM_005228	1
-    chr7	140753274	140753394	NM_004333	1
+	55173921	55174041	NM_005228	1
+	55174711	55174831	NM_005228	1
+	55181292	55181478	NM_005228	1
+	55191718	55191874	NM_005228	1
+	140753274	140753394	NM_004333	1

Bunch of modification from Jacques #8

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Merged

SimCab-CHU merged 12 commits into SimCab-CHU:main from Juke34:jd

Jun 13, 2025

-Original file line number
+Diff line change
@@ -0,0 +1,62 @@
+    # This is a basic workflow to help you get started with Actions
+    name: CI
+    # Controls when the action will run.
+    # Triggers the workflow on push or pull request events
+    on: [push, pull_request, workflow_dispatch]
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: true
+    # A workflow run is made up of one or more jobs that can run sequentially or in parallel
+    jobs:
+      # This workflow contains a second job called "build2"
+      test_MobiCT:
+        # avoid to run twice push and PR
+        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+        # The type of runner that the job will run on
+        runs-on: ubuntu-24.04
+        services:
+          docker:
+            image: docker:dind
+            options: --privileged --shm-size=2g
+            volumes:
+              - /var/run/docker.sock:/var/run/docker.sock:ro
+        # Steps represent a sequence of tasks that will be executed as part of the job
+        steps:
+          # Install/cache OpenJDK
+          - name: Cache OpenJDK
+            id: cache-openjdk
+            uses: actions/cache@v3
+            with:
+              path: /usr/lib/jvm/java-11-openjdk-amd64
+              key: ${{ runner.os }}-openjdk-11
+              restore-keys: |
+                ${{ runner.os }}-openjdk-11
+          - name: Install openjdk
+            if: ${{ steps.cache-openjdk.outputs.cache-hit != 'true' }}
+            run: sudo apt-get install openjdk-11-jdk
+          # Install/cache nextflow
+          - name: Cache nextflow
+            id: cache-nextflow
+            uses: actions/cache@v3
+            with:
+              path: /usr/local/bin/nextflow
+              key: ${{ runner.os }}-nextflow
+              restore-keys: |
+                ${{ runner.os }}-nextflow
+          - name: Install Nextflox
+            if: ${{ steps.cache-nextflow.outputs.cache-hit != 'true' }}
+            run: curl -s https://get.nextflow.io | bash && mv nextflow /usr/local/bin && chmod +x /usr/local/bin/nextflow
+          # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+          - uses: actions/checkout@v3
+          # Run tests sequentialy
+          - name: test
+            run: nextflow run -ansi-log -profile docker,test,ci MobiCT.nf

-Original file line number
+Diff line change
@@ -1,8 +1,5 @@
-    chr12	25245268	25245388	NM_033360	1
-    chr15	90088586	90088747	NM_002168	1
-    chr2	208248368	208248660	NM_005896	1
-    chr7	55173921	55174041	NM_005228	1
-    chr7	55174711	55174831	NM_005228	1
-    chr7	55181292	55181478	NM_005228	1
-    chr7	55191718	55191874	NM_005228	1
-    chr7	140753274	140753394	NM_004333	1
+	55173921	55174041	NM_005228	1
+	55174711	55174831	NM_005228	1
+	55181292	55181478	NM_005228	1
+	55191718	55191874	NM_005228	1
+	140753274	140753394	NM_004333	1

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