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LilyAnderssonLeeLilyAnderssonLee
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Merge pull request #88 from genomic-medicine-sweden/keepalive_api
add keepalive api to keep repo active
2 parents 0c599b9 + 820212a commit d7ecb6d

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‎.github/workflows/build_dockerfile_pangolin_master.yml

+73-65
Original file line numberDiff line numberDiff line change
@@ -1,84 +1,92 @@
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name: Build and publish pangolin docker image for master
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on:
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schedule:
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- cron: '0 0 * * *'
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push:
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schedule:
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- cron: "0 0 * * *"
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push:
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branches:
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- master
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jobs:
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get-version:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Get current date
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id: date
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run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
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- name: Test with environment variables
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run: echo $RELEASE_DATE
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env:
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RELEASE_DATE: ${{ steps.date.outputs.date }}
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- name: Fetch pangolin version
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shell: bash
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run: |
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##Get pangolin-data version
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curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \
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jq -r ".tag_name" > versions/pangolin-data-latest-version.txt
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pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt)
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echo $pangolin_data_VER
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- uses: actions/checkout@v2
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- name: Get current date
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id: date
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run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
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- name: Test with environment variables
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run: echo $RELEASE_DATE
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env:
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RELEASE_DATE: ${{ steps.date.outputs.date }}
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- name: Fetch pangolin version
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shell: bash
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run: |
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##Get pangolin-data version
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curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \
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jq -r ".tag_name" > versions/pangolin-data-latest-version.txt
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pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt)
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echo $pangolin_data_VER
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##Get constellations version
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curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \
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jq -r ".tag_name" > versions/constellations-latest-version.txt
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constellations_VER=$(cat versions/constellations-latest-version.txt)
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echo $constellations_VER
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##Get constellations version
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curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \
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jq -r ".tag_name" > versions/constellations-latest-version.txt
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constellations_VER=$(cat versions/constellations-latest-version.txt)
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echo $constellations_VER
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##Get pangolin version
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curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \
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jq -r ".tag_name" > versions/pangolin-latest-version.txt
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PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt)
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echo $PANGOLIN_VER
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##Get pangolin version
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curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \
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jq -r ".tag_name" > versions/pangolin-latest-version.txt
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PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt)
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echo $PANGOLIN_VER
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##Get scorpio version
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curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \
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jq -r ".tag_name" > versions/scorpio-latest-version.txt
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scorpio_VER=$(cat versions/scorpio-latest-version.txt)
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echo $scorpio_VER
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##Get scorpio version
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curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \
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jq -r ".tag_name" > versions/scorpio-latest-version.txt
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scorpio_VER=$(cat versions/scorpio-latest-version.txt)
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echo $scorpio_VER
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- name: Check for modified files
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id: git-check
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run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true")
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- name: Check for modified files
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id: git-check
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run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true")
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- name: Login to Docker Hub
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uses: docker/login-action@v1
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with:
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username: ${{ secrets.DOCKER_HUB_USERNAME }}
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password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
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- name: Login to Docker Hub
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uses: docker/login-action@v1
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with:
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username: ${{ secrets.DOCKER_HUB_USERNAME }}
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password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
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- name: Set up Docker Buildx
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id: buildx
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uses: docker/setup-buildx-action@v1
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- name: Set up Docker Buildx
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id: buildx
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uses: docker/setup-buildx-action@v1
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- name: Build new docker image
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shell: bash
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run: |
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echo ${{ steps.date.outputs.date }}
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REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
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pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
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scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
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constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
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#Build docker for pangolin-check for specific requirements
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docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin:latest -t genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
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- name: Build new docker image
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shell: bash
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run: |
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echo ${{ steps.date.outputs.date }}
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REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
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pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
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scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
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constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
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#Build docker for pangolin-check for specific requirements
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docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin:latest -t genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
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- name: Push Docker image to DockerHub
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shell: bash
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run: |
77+
REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
78+
pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
79+
scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
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constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
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#Push to dockerhub for pangolin with specific requirements
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docker image push genomicmedicinesweden/gms-artic-pangolin:latest
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docker image push genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
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- name: Push Docker image to DockerHub
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shell: bash
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run: |
78-
REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
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pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
80-
scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
81-
constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
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#Push to dockerhub for pangolin with specific requirements
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docker image push genomicmedicinesweden/gms-artic-pangolin:latest
84-
docker image push genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
85+
keepalive-job:
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name: Keepalive Workflow
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runs-on: ubuntu-latest
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permissions:
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actions: write
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steps:
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- uses: actions/checkout@v2
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- uses: gautamkrishnar/keepalive-workflow@v2

‎.github/workflows/build_dockerfile_pangolin_stage.yml

+70-62
Original file line numberDiff line numberDiff line change
@@ -6,74 +6,82 @@ jobs:
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get-version:
77
runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
10-
- name: Get current date
11-
id: date
12-
run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
13-
- name: Test with environment variables
14-
run: echo $RELEASE_DATE
15-
env:
16-
RELEASE_DATE: ${{ steps.date.outputs.date }}
17-
- name: Fetch pangolin version
18-
shell: bash
19-
run: |
20-
##Get pangolin-data version
21-
curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \
22-
jq -r ".tag_name" > versions/pangolin-data-latest-version.txt
23-
pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt)
24-
echo $pangolin_data_VER
9+
- uses: actions/checkout@v2
10+
- name: Get current date
11+
id: date
12+
run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
13+
- name: Test with environment variables
14+
run: echo $RELEASE_DATE
15+
env:
16+
RELEASE_DATE: ${{ steps.date.outputs.date }}
17+
- name: Fetch pangolin version
18+
shell: bash
19+
run: |
20+
##Get pangolin-data version
21+
curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \
22+
jq -r ".tag_name" > versions/pangolin-data-latest-version.txt
23+
pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt)
24+
echo $pangolin_data_VER
2525
26-
##Get constellations version
27-
curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \
28-
jq -r ".tag_name" > versions/constellations-latest-version.txt
29-
constellations_VER=$(cat versions/constellations-latest-version.txt)
30-
echo $constellations_VER
26+
##Get constellations version
27+
curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \
28+
jq -r ".tag_name" > versions/constellations-latest-version.txt
29+
constellations_VER=$(cat versions/constellations-latest-version.txt)
30+
echo $constellations_VER
3131
32-
##Get pangolin version
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curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \
34-
jq -r ".tag_name" > versions/pangolin-latest-version.txt
35-
PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt)
36-
echo $PANGOLIN_VER
32+
##Get pangolin version
33+
curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \
34+
jq -r ".tag_name" > versions/pangolin-latest-version.txt
35+
PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt)
36+
echo $PANGOLIN_VER
3737
38-
##Get scorpio version
39-
curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \
40-
jq -r ".tag_name" > versions/scorpio-latest-version.txt
41-
scorpio_VER=$(cat versions/scorpio-latest-version.txt)
42-
echo $scorpio_VER
38+
##Get scorpio version
39+
curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \
40+
jq -r ".tag_name" > versions/scorpio-latest-version.txt
41+
scorpio_VER=$(cat versions/scorpio-latest-version.txt)
42+
echo $scorpio_VER
4343
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- name: Check for modified files
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id: git-check
46+
run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true")
4447

45-
- name: Check for modified files
46-
id: git-check
47-
run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true")
48+
- name: Login to Docker Hub
49+
uses: docker/login-action@v1
50+
with:
51+
username: ${{ secrets.DOCKER_HUB_USERNAME }}
52+
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
4853

49-
- name: Login to Docker Hub
50-
uses: docker/login-action@v1
51-
with:
52-
username: ${{ secrets.DOCKER_HUB_USERNAME }}
53-
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
54+
- name: Set up Docker Buildx
55+
id: buildx
56+
uses: docker/setup-buildx-action@v1
5457

55-
- name: Set up Docker Buildx
56-
id: buildx
57-
uses: docker/setup-buildx-action@v1
58+
- name: Build new docker image
59+
shell: bash
60+
run: |
61+
echo ${{ steps.date.outputs.date }}
62+
REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
63+
pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
64+
scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
65+
constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
66+
#Build docker for pangolin-check for specific requirements
67+
docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin-stage:latest -t genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
5868
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- name: Build new docker image
60-
shell: bash
61-
run: |
62-
echo ${{ steps.date.outputs.date }}
63-
REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
64-
pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
65-
scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
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constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
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#Build docker for pangolin-check for specific requirements
68-
docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin-stage:latest -t genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} .
69+
- name: Push Docker image to DockerHub
70+
shell: bash
71+
run: |
72+
REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
73+
pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
74+
scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
75+
constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
76+
#Push to dockerhub for pangolin with specific requirements
77+
docker image push genomicmedicinesweden/gms-artic-pangolin-stage:latest
78+
docker image push genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}
6979
70-
- name: Push Docker image to DockerHub
71-
shell: bash
72-
run: |
73-
REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||')
74-
pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||')
75-
scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||')
76-
constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
77-
#Push to dockerhub for pangolin with specific requirements
78-
docker image push genomicmedicinesweden/gms-artic-pangolin-stage:latest
79-
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}
80+
keepalive-job:
81+
name: Keepalive Workflow
82+
runs-on: ubuntu-latest
83+
permissions:
84+
actions: write
85+
steps:
86+
- uses: actions/checkout@v2
87+
- uses: gautamkrishnar/keepalive-workflow@v2

‎workflows/articNcovNanopore.nf

+2-2
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ include {versions} from '../modules/analysis.nf'
2121
include {pangoversions} from '../modules/analysis.nf'
2222
include {fastqcNanopore} from '../modules/qc.nf'
2323
include {multiqcNanopore} from '../modules/qc.nf'
24-
include {pycoqc} from '../modules/qc.nf'
24+
//include {pycoqc} from '../modules/qc.nf'
2525

2626
include {bamToCram} from '../modules/out.nf'
2727

@@ -46,7 +46,7 @@ workflow sequenceAnalysisNanopolish {
4646

4747
multiqcNanopore(fastqcNanopore.out.zip)
4848

49-
pycoqc(ch_seqSummary)
49+
//pycoqc(ch_seqSummary)
5050

5151
articDownloadScheme()
5252

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