configure github actions jobs to succeed on timeout and set up references (95366340) · Commits · github_fork / Universc

.gitattributes

+6 −0

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		@@ -59,3 +59,9 @@ test/shared/indrop-v3-test/Undetermined_S0_L001_R3_001.fastq filter=lfs diff=lfs
		test/shared/indrop-v3-test/Undetermined_S0_L001_R4_001.fastq filter=lfs diff=lfs merge=lfs -text
		test/shared/indrop-v3-test/Undetermined_S0_L002_R1_001.fastq filter=lfs diff=lfs merge=lfs -text
		test/shared/indrop-v3-test/Undetermined_S0_L002_R2_001.fastq filter=lfs diff=lfs merge=lfs -text
		test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/smartseq3-test/Smartseq3_diySpike_I1.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/smartseq3-test/Smartseq3_diySpike_I2.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text

.github/workflows/docker-test-10x.yml

+14 −6

Original line number	Diff line number	Diff line
		@@ -36,12 +36,14 @@ jobs:
		image: tomkellygenetics/universc:latest
		run: echo "hello from universc"
		- name: Call UniverSC from image
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh
		timeout-minutes: 15
		run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
		- name: Call UniverSC from container
		timeout-minutes: 15
		uses: addnab/docker-run-action@v1
		with:
		image: tomkellygenetics/universc:latest
		run: bash /universc/test/run_tests_10x_gh_actions.sh
		run: timeout 10 bash /universc/test/run_tests_10x_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

		build:
		runs-on: ubuntu-20.04
		@@ -70,8 +72,12 @@ jobs:
		file: ./Dockerfile
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: false
		- name: Test 10x timeout
		timeout-minutes: 10
		run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_cellranger_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
		- name: Test 10x
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh
		timeout-minutes: 10
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_cellranger_gh_actions.sh

		test-10x-v2:
		runs-on: ubuntu-20.04
		@@ -92,7 +98,8 @@ jobs:
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: false
		- name: Test 10x
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_v2_gh_actions.sh
		timeout-minutes: 15
		run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_v2_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

		test-10x:
		runs-on: ubuntu-20.04
		@@ -113,4 +120,5 @@ jobs:
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: false
		- name: Test 10x
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh
		timeout-minutes: 15
		run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

.github/workflows/docker-test-dropseq.yml

+1 −1

Original line number	Diff line number	Diff line
		@@ -29,4 +29,4 @@ jobs:
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: false
		- name: Test DropSeq
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_dropseq_gh_actions.sh
		run: timeout 60 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_dropseq_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

.github/workflows/docker-test-icell8.yml

+1 −1

Original line number	Diff line number	Diff line
		@@ -29,4 +29,4 @@ jobs:
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: false
		- name: Test ICELL8
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_icell8_gh_actions.sh
		run: timeout 15 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_icell8_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

.github/workflows/docker-test-indropsv3.yml

+1 −1

Original line number	Diff line number	Diff line
		@@ -29,4 +29,4 @@ jobs:
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: false
		- name: Test inDrops v3
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_indropsv3_gh_actions.sh
		run: timeout 30 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_indropsv3_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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