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adds custom parameters (STRT-Seq-2018 technology) for Fan et al., (20…

adds custom parameters (STRT-Seq-2018 technology) for Fan et al., (20… #270

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name: Run all tests in Docker
on: workflow_dispach
jobs:
test:
runs-on: ubuntu-20.04
steps:
-
name: Login to DockerHub
uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
build:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
run:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: Hello world
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test echo "hello world"
- name: Diagnostics
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd;ls
call:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: Test call
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test bash /universc/test/test_call.sh
test-10x-v2:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: clear environment
run: rm -rf *
- name: Test 10x
timeout-minutes: 300
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi
test-10x-v3:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: clear environment
run: rm -rf *
- name: Test 10x
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi
test-cellranger:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: clear environment
run: rm -rf *
- name: Test Cell Ranger
timeout-minutes: 45
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m /universc/test/run_tests_cellranger_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi
test-dropseq:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: clear environment
run: rm -rf *
- name: Test DropSeq
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 45m /universc/test/run_tests_dropseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi
test-icell8:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: clear environment
run: rm -rf *
- name: Test ICELL8
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m /universc/test/run_tests_icell8_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
test-indrops-v3:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: clear environment
run: rm -rf *
- name: Test inDrops v3
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m /universc/test/run_tests_indropsv3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
test-sci-seq:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: clear environment
run: rm -rf *
- name: Test SCI-Seq3
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m /universc/test/run_tests_sciseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
test-smart-seq3:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: docker/setup-buildx-action@v1
- uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
registry: ${{ env.REGISTRY }}
- name: Build and push
uses: docker/build-push-action@v2
with:
context: ./
file: ./Dockerfile
tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
push: false
- name: clear environment
run: rm -rf *
- name: Test Smart-Seq3
run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m /universc/test/run_tests_smartseq3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi