Commit 3326fc25 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct inputs for tests on GitHub actions

parent b2aff8ba

.github/workflows/docker-run-tests.yml

+23 −21
Original line number Diff line number Diff line 


name: Run all tests in Docker

on: push

jobs:
@@ -74,7 +75,7 @@ jobs: 
    - name: Test call

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/test_call.sh



  test-cellranger:

  test-10x-v2:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2
@@ -94,11 +95,11 @@ jobs: 
        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test Cell Ranger

      timeout-minutes: 45      

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_cellranger_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

    - name: Test 10x

      timeout-minutes: 300

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 20m bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi



  test-10x-v2:

  test-10x-v3:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2
@@ -119,10 +120,9 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 300

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 20m bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi



  test-10x-v3:

  test-cellranger:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2
@@ -142,8 +142,9 @@ jobs: 
        push: false 

    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

    - name: Test Cell Ranger

      timeout-minutes: 45      

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_cellranger_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi



  test-dropseq:

    runs-on: ubuntu-20.04
@@ -191,7 +192,7 @@ jobs: 
    - name: Test ICELL8

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_icell8_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-smart-seq3:

  test-indrops-v3:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2
@@ -211,10 +212,10 @@ jobs: 
        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test Smart-Seq3

      run: run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_smartseq3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

    - name: Test inDrops v3

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_indropsv3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-indrops-v3:

  test-sci-seq:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2
@@ -234,10 +235,10 @@ jobs: 
        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test inDrops v3

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_indropsv3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

    - name: Test SCI-Seq3

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_sciseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-sci-seq:

  test-smart-seq3:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2
@@ -257,5 +258,6 @@ jobs: 
        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test SCI-Seq3

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_sciseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
 
    - name: Test Smart-Seq3

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_smartseq3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

test/run_tests_dropseq_gh_actions.sh

+8 −8
Original line number Diff line number Diff line
@@ -10,14 +10,14 @@ export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH 
cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

cd test/cellranger_reference/cellranger-tiny-ref/

cellranger mkref --genome=3.0.0 --fasta=genome-3.0.0.fa --genes=genes-3.0.0.gtf

cd ../../..

make -C test/cellranger_reference/cellranger-tiny-ref reference 

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0



rm -rf test/shared/dropseq-test/* test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ test/shared/sciseq-v3-test

#rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

#cd test/cellranger_reference/cellranger-tiny-ref/

#cellranger mkref --genome=3.0.0 --fasta=genome-3.0.0.fa --genes=genes-3.0.0.gtf

#cd ../../..

#make -C test/cellranger_reference/cellranger-tiny-ref reference 

#rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0



#rm -rf test/shared/dropseq-test/* test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ test/shared/sciseq-v3-test



# test manual setup

bash launch_universc.sh -t "nadia" --setup

test/run_tests_indropsv3_gh_actions.sh

+1 −1
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ cellrangerpath=`which cellranger` 
rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

cd test/cellranger_reference/cellranger-tiny-ref/

cellranger mkref --genome=3.0.0 --fasta=genome-3.0.0.fa --genes=genes-3.0.0.gtf

../../..

cd ../../..

make -C test/cellranger_reference/cellranger-tiny-ref reference

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0

test/run_tests_sciseq_gh_actions.sh

+2 −2
Original line number Diff line number Diff line
@@ -21,6 +21,6 @@ rm -rf test/shared/dropseq-test/* test/shared/cellranger-tiny-fastq/* test/shar 


bash launch_universc.sh --id "test-sciseq" --technology "sciseq" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/sciseq-v3-test/SRR7827205_S1_R1.fastq" \

 --read2 "test/shared/sciseq-v3-test/SRR7827205_S1_R2.fastq" \

 --read1 "test/shared/sciseq-v3-test/SRR7827205_S1_R1.fastq.gz" \

 --read2 "test/shared/sciseq-v3-test/SRR7827205_S1_R2.fastq.gz" \

 --jobmode "local" --localcores 1

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