32 include the automatic generation of a samplesheet for mpgap #30
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # This workflow set's up an automated execution for testing the code when a new PR is created | |
| # It uses the head branch name to trigger the execution of the new module or subworkflow ... | |
| # | |
| # For example, if I just created a module for roary, I should name the new branch as roary | |
| # then, this workflow will run: nextflow run fmalmeida/bacannot-compare --roary (the head branch name) [blah blah blah] | |
| name: Testing pacbio / singularity from PR | |
| on: | |
| pull_request: | |
| branches: [ master, dev ] | |
| types: [ opened, synchronize, reopened ] | |
| jobs: | |
| run_nextflow: | |
| name: Run pipeline for the upcoming PR | |
| runs-on: ubuntu-latest | |
| env: | |
| DOCKERHUB_USERNAME: ${{ secrets.DOCKER_USER }} | |
| DOCKERHUB_PASS: ${{ secrets.DOCKER_PASSWORD }} | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.3 | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Clean environment | |
| run: | | |
| sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android | |
| sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET | |
| - name: Run tests for pacbio | |
| run: | | |
| wget https://downloads.pacbcloud.com/public/dataset/MicrobialMultiplexing_48plex/48-plex_bam/lima.bc1040--bc1040.bam.gz | |
| gzip -d lima.bc1040--bc1040.bam.gz | |
| nextflow run main.nf \ | |
| -profile singularity \ | |
| --max_cpus 2 \ | |
| --output TEST_DIR \ | |
| --pacbio_bam "lima.bc1040--bc1040.bam" \ | |
| --pacbio_get_hifi | |
| rm -r work .nextflow* | |
| - name: View results | |
| run: | | |
| sudo apt-get install -y tree | |
| tree TEST_DIR |