Add .github/workflows/ci.yml for implementing CI/CD

[cgpu]

NOTE: GitHub actions requires additional configuration for running on GPU instances. It is recommended to implement first the cpu only mode.

There are also limitations in the resources that can be used when testing with Github Actions:

Hardware specification for Linux virtual machines (used by default) https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources

Max cpus: 2-core CPU Max memory: 7 GB of RAM memory Max disk size: 14 GB of SSD disk space

To be able to add CI/CD successfully therefore, a minimal test dataset is required.

Here is the template file that implements both docker and singularity CI. It needs to be created in a folder in the root of the repo named .github/workflows/ci.yml (the folder names are reserved, the file name can be changed eg for ci.yml to continues-integration.yml etc)

name: splicing-pipelines-nf CI
# This workflow is triggered on pushes and PRs to the repository.
on: [pull_request]

jobs:
  docker:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        nxf_ver: ['20.01.0', '']
    steps:
      - uses: actions/checkout@v1
      - name: Install Nextflow
        run: |
          export NXF_VER=${{ matrix.nxf_ver }}
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Basic workflow tests
        run: |
          nextflow run ${GITHUB_WORKSPACE} --config conf/test.config
  singularity:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        singularity_version: ['3.6.4']
        nxf_ver: ['20.01.0', '']
    steps:
      - uses: actions/checkout@v1
      - uses: eWaterCycle/setup-singularity@v6
        with:
          singularity-version: ${{ matrix.singularity_version }}
      - name: Install Nextflow
        run: |
          export NXF_VER=${{ matrix.nxf_ver }}
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Basic workflow tests
        run: |
          nextflow run ${GITHUB_WORKSPACE}  --config conf/test.config

Many configs can be tested using the matrix stretegy.

[liuyang2006]

Docker test has been passed, we will add singularity test after we push singularity image into a public portal.

[liuyang2006]

Achieved by https://github.com/TheJacksonLaboratory/nanome/pull/108. Results can be found here: https://github.com/TheJacksonLaboratory/nanome/actions/runs/1283587877.