Trim "Undetermined" fastq and change dir name "pipeline_info" #94
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| name: CI (human PE UST and ST data) | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| # It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Nextflow versions: check pipeline minimum and current latest | |
| nxf_ver: [''] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Crean env | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Pull docker image | |
| run: | | |
| docker pull myoshimura080822/ramdaq:v1.2 | |
| - name: Run pipeline with test_PE_UST_H | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_PE_UST_H,docker --genome GRCh38_v41_chr19 --entire_max_cpus 2 --entire_max_memory '4.GB' | |
| sudo rm -rf /home/runner/work/ramdaq/ramdaq/results/pipeline_info | |
| - name: Run pipeline with test_PE_ST_H | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_PE_ST_H,docker --genome GRCh38_v41_chr19 --entire_max_cpus 2 --entire_max_memory '4.GB' | |
| sudo rm -rf /home/runner/work/ramdaq/ramdaq/results/pipeline_info | |
| - name: Deploy to ramdaq-human-pe-ust.surge.sh | |
| uses: dswistowski/surge-sh-action@v1 | |
| with: | |
| domain: 'ramdaq-human-pe-ust.surge.sh' | |
| project: './results_PE_UST_H/MultiQC' | |
| login: ${{ secrets.SURGE_LOGIN }} | |
| token: ${{ secrets.SURGE_TOKEN }} | |
| - name: Deploy to ramdaq-human-pe-st.surge.sh | |
| uses: dswistowski/surge-sh-action@v1 | |
| with: | |
| domain: 'ramdaq-human-pe-st.surge.sh' | |
| project: './results_PE_ST_H/MultiQC' | |
| login: ${{ secrets.SURGE_LOGIN }} | |
| token: ${{ secrets.SURGE_TOKEN }} |