Merge pull request #88 from genomic-medicine-sweden/keepalive_api

add keepalive api to keep repo active
genomic-medicine-sweden · Sep 5, 2024 · d7ecb6d · d7ecb6d
2 parents 0c599b9 + 820212a
commit d7ecb6d
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diff --git a/.github/workflows/build_dockerfile_pangolin_master.yml b/.github/workflows/build_dockerfile_pangolin_master.yml
@@ -1,84 +1,92 @@
 name: Build and publish pangolin docker image for master
 
 on:
- schedule:
-   - cron: '0 0 * * *'
- push:
+  schedule:
+    - cron: "0 0 * * *"
+  push:
     branches:
       - master
 
 jobs:
   get-version:
     runs-on: ubuntu-latest
     steps:
-     - uses: actions/checkout@v2
-     - name: Get current date
-       id: date
-       run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
-     - name: Test with environment variables
-       run: echo $RELEASE_DATE
-       env:
-         RELEASE_DATE: ${{ steps.date.outputs.date }}
-     - name: Fetch pangolin version
-       shell: bash
-       run: |
-         ##Get pangolin-data version
-         curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \
-         jq -r ".tag_name" > versions/pangolin-data-latest-version.txt
-         pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt)
-         echo $pangolin_data_VER
+      - uses: actions/checkout@v2
+      - name: Get current date
+        id: date
+        run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
+      - name: Test with environment variables
+        run: echo $RELEASE_DATE
+        env:
+          RELEASE_DATE: ${{ steps.date.outputs.date }}
+      - name: Fetch pangolin version
+        shell: bash
+        run: |
+          ##Get pangolin-data version
+          curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \
+          jq -r ".tag_name" > versions/pangolin-data-latest-version.txt
+          pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt)
+          echo $pangolin_data_VER
 
-         ##Get constellations version
-         curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \
-         jq -r ".tag_name" > versions/constellations-latest-version.txt
-         constellations_VER=$(cat versions/constellations-latest-version.txt)
-         echo $constellations_VER
+          ##Get constellations version
+          curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \
+          jq -r ".tag_name" > versions/constellations-latest-version.txt
+          constellations_VER=$(cat versions/constellations-latest-version.txt)
+          echo $constellations_VER
 
-         ##Get pangolin version
-         curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \
-         jq -r ".tag_name" > versions/pangolin-latest-version.txt
-         PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt)
-         echo $PANGOLIN_VER
+          ##Get pangolin version
+          curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \
+          jq -r ".tag_name" > versions/pangolin-latest-version.txt
+          PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt)
+          echo $PANGOLIN_VER
 
-         ##Get scorpio version
-         curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \
-         jq -r ".tag_name" > versions/scorpio-latest-version.txt
-         scorpio_VER=$(cat versions/scorpio-latest-version.txt)
-         echo $scorpio_VER
+          ##Get scorpio version
+          curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \
+          jq -r ".tag_name" > versions/scorpio-latest-version.txt
+          scorpio_VER=$(cat versions/scorpio-latest-version.txt)
+          echo $scorpio_VER
 
+      - name: Check for modified files
+        id: git-check
+        run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true")
 
-     - name: Check for modified files
-       id: git-check
-       run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true")
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
-     - name: Login to Docker Hub
-       uses: docker/login-action@v1
-       with:
-         username: ${{ secrets.DOCKER_HUB_USERNAME }}
-         password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v1
 
-     - name: Set up Docker Buildx
-       id: buildx
-       uses: docker/setup-buildx-action@v1
+      - name: Build new docker image
+        shell: bash
+        run: |
+          echo  ${{ steps.date.outputs.date }}
+          REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
+          pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
+          scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
+          constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
+          #Build docker for pangolin-check for specific requirements
+          docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin:latest -t genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
 
-     - name: Build new docker image
-       shell: bash
-       run: |
-         echo  ${{ steps.date.outputs.date }}
-         REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
-         pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
-         scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
-         constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
-         #Build docker for pangolin-check for specific requirements
-         docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin:latest -t genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
+      - name: Push Docker image to DockerHub
+        shell: bash
+        run: |
+          REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
+          pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
+          scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
+          constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
+          #Push to dockerhub for pangolin with specific requirements
+          docker image push genomicmedicinesweden/gms-artic-pangolin:latest
+          docker image push genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
 
-     - name: Push Docker image to DockerHub
-       shell: bash
-       run: |
-         REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
-         pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
-         scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
-         constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
-         #Push to dockerhub for pangolin with specific requirements
-         docker image push genomicmedicinesweden/gms-artic-pangolin:latest
-         docker image push genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
+  keepalive-job:
+    name: Keepalive Workflow
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write
+    steps:
+      - uses: actions/checkout@v2
+      - uses: gautamkrishnar/keepalive-workflow@v2
diff --git a/.github/workflows/build_dockerfile_pangolin_stage.yml b/.github/workflows/build_dockerfile_pangolin_stage.yml
@@ -6,74 +6,82 @@ jobs:
   get-version:
     runs-on: ubuntu-latest
     steps:
-     - uses: actions/checkout@v2
-     - name: Get current date
-       id: date
-       run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
-     - name: Test with environment variables
-       run: echo $RELEASE_DATE
-       env:
-         RELEASE_DATE: ${{ steps.date.outputs.date }}
-     - name: Fetch pangolin version
-       shell: bash
-       run: |
-         ##Get pangolin-data version
-         curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \
-         jq -r ".tag_name" > versions/pangolin-data-latest-version.txt
-         pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt)
-         echo $pangolin_data_VER
+      - uses: actions/checkout@v2
+      - name: Get current date
+        id: date
+        run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
+      - name: Test with environment variables
+        run: echo $RELEASE_DATE
+        env:
+          RELEASE_DATE: ${{ steps.date.outputs.date }}
+      - name: Fetch pangolin version
+        shell: bash
+        run: |
+          ##Get pangolin-data version
+          curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \
+          jq -r ".tag_name" > versions/pangolin-data-latest-version.txt
+          pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt)
+          echo $pangolin_data_VER
 
-         ##Get constellations version
-         curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \
-         jq -r ".tag_name" > versions/constellations-latest-version.txt
-         constellations_VER=$(cat versions/constellations-latest-version.txt)
-         echo $constellations_VER
+          ##Get constellations version
+          curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \
+          jq -r ".tag_name" > versions/constellations-latest-version.txt
+          constellations_VER=$(cat versions/constellations-latest-version.txt)
+          echo $constellations_VER
 
-         ##Get pangolin version
-         curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \
-         jq -r ".tag_name" > versions/pangolin-latest-version.txt
-         PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt)
-         echo $PANGOLIN_VER
+          ##Get pangolin version
+          curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \
+          jq -r ".tag_name" > versions/pangolin-latest-version.txt
+          PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt)
+          echo $PANGOLIN_VER
 
-         ##Get scorpio version
-         curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \
-         jq -r ".tag_name" > versions/scorpio-latest-version.txt
-         scorpio_VER=$(cat versions/scorpio-latest-version.txt)
-         echo $scorpio_VER
+          ##Get scorpio version
+          curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \
+          jq -r ".tag_name" > versions/scorpio-latest-version.txt
+          scorpio_VER=$(cat versions/scorpio-latest-version.txt)
+          echo $scorpio_VER
 
+      - name: Check for modified files
+        id: git-check
+        run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true")
 
-     - name: Check for modified files
-       id: git-check
-       run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true")
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
-     - name: Login to Docker Hub
-       uses: docker/login-action@v1
-       with:
-         username: ${{ secrets.DOCKER_HUB_USERNAME }}
-         password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v1
 
-     - name: Set up Docker Buildx
-       id: buildx
-       uses: docker/setup-buildx-action@v1
+      - name: Build new docker image
+        shell: bash
+        run: |
+          echo  ${{ steps.date.outputs.date }}
+          REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
+          pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
+          scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
+          constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
+          #Build docker for pangolin-check for specific requirements
+          docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin-stage:latest -t genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
 
-     - name: Build new docker image
-       shell: bash
-       run: |
-         echo  ${{ steps.date.outputs.date }}
-         REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
-         pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
-         scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
-         constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
-         #Build docker for pangolin-check for specific requirements
-         docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin-stage:latest -t genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
+      - name: Push Docker image to DockerHub
+        shell: bash
+        run: |
+          REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
+          pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
+          scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
+          constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
+          #Push to dockerhub for pangolin with specific requirements
+          docker image push genomicmedicinesweden/gms-artic-pangolin-stage:latest
+          docker image push genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
 
-     - name: Push Docker image to DockerHub
-       shell: bash
-       run: |
-         REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
-         pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
-         scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
-         constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
-         #Push to dockerhub for pangolin with specific requirements
-         docker image push genomicmedicinesweden/gms-artic-pangolin-stage:latest
-         docker image push genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
+  keepalive-job:
+    name: Keepalive Workflow
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write
+    steps:
+      - uses: actions/checkout@v2
+      - uses: gautamkrishnar/keepalive-workflow@v2
diff --git a/workflows/articNcovNanopore.nf b/workflows/articNcovNanopore.nf
@@ -21,7 +21,7 @@ include {versions} from '../modules/analysis.nf'
 include {pangoversions} from '../modules/analysis.nf'
 include {fastqcNanopore} from '../modules/qc.nf'
 include {multiqcNanopore} from '../modules/qc.nf'
-include {pycoqc} from '../modules/qc.nf'
+//include {pycoqc} from '../modules/qc.nf'
 
 include {bamToCram} from '../modules/out.nf'
 
@@ -46,7 +46,7 @@ workflow sequenceAnalysisNanopolish {
 
       multiqcNanopore(fastqcNanopore.out.zip)
 
-      pycoqc(ch_seqSummary)
+      //pycoqc(ch_seqSummary)
 
       articDownloadScheme()