install.yml

name: Install

on: [push, pull_request]

jobs:

  skip_duplicate:
    permissions:
      actions: write
      contents: read
    runs-on: ubuntu-latest
    outputs:
      should_skip: ${{ steps.skip_check.outputs.should_skip }}
    steps:
      - id: skip_check
        uses: fkirc/skip-duplicate-actions@v5.3.0
        with:
          cancel_others: 'true'
          concurrent_skipping: 'same_content_newer'

  Install:
    needs: skip_duplicate
    if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }}
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
      - name: Setup mamba
        uses: conda-incubator/setup-miniconda@v3
        with:
          mamba-version: "*"
          channels: conda-forge,bioconda,defaults
          auto-activate-base: true
          activate-environment: ""
      - name: Install Snakemake 7.32
        run: |
          pip install snakemake=7.32
      - name: Create environments
        run: |
          snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --conda-create-envs-only --use-conda

  Dry_run:
    needs: skip_duplicate
    if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }}
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
      - name: Setup mamba
        uses: conda-incubator/setup-miniconda@v3
        with:
          mamba-version: "*"
          channels: conda-forge,bioconda,defaults
          auto-activate-base: true
          activate-environment: ""
      - name: Install Snakemake 7.32
        run: |
          pip install snakemake=7.32
      - name: Dry run
        run: |
          snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --dry-run