ci.yml

name: CI

# Controls when the action will run. 
on:
  # Triggers the workflow on push or pull request events but only for the master branch
  push:
    branches: [ master ]
    paths-ignore:
      - README.md
      - CHANGES.md
      - .gitpod.yml
      - 'docs/**'
      - 'setup/**'
      - 'env/*'
  pull_request:
    branches: [ master ]
    paths-ignore:
      - README.md
      - CHANGES.md
      - .gitpod.yml
      - 'docs/**'
      - 'setup/**'
      - 'env/*'

  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

jobs:

  # Downloads exemplar data from S3 as needed
  setup:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Install Nextflow
        run: curl -fsSL get.nextflow.io | bash

      # Exemplars will be cached
      - name: Exemplar-001 cache
        uses: actions/cache@v3
        id: cache-ex001
        with:
          path: ~/data/exemplar-001
          key: ex001-2022-02-24
      - name: Exemplar-001 (w/ autofluorescence) cache
        uses: actions/cache@v3
        id: cache-ex001-af
        with:
          path: ~/data/af/exemplar-001
          key: ex001-af-2023-01-14
      - name: Exemplar-002 cache
        uses: actions/cache@v3
        id: cache-ex002
        with:
          path: ~/data/exemplar-002
          key: ex002-2022-02-24

      # Download data only if no cache is available
      - name: Exemplar-001 download
        if: steps.cache-ex001.outputs.cache-hit != 'true'
        run: ./nextflow exemplar.nf --name exemplar-001 --path ~/data
      - name: Exemplar-001 (w/ autofluorescence) download
        if: steps.cache-ex001-af.outputs.cache-hit != 'true'
        run: ./nextflow exemplar.nf --name exemplar-001 --path ~/data/af --from-cycle 1 --to-cycle 3
      - name: Exemplar-002 download
        if: steps.cache-ex002.outputs.cache-hit != 'true'
        run: ./nextflow exemplar.nf --name exemplar-002 --path ~/data --from-cycle 6 --to-cycle 7

  # Test exemplar-001
  ex001:
    strategy:
      matrix:
        params:
          - --viz
          - --start-at illumination --stop-at registration
          - --background
          - --background --background-method imagej-rolling-ball
          - --segmentation cypository --cypository-opts '--channel 10 --scalingFactor 2' --s3seg-opts '--logSigma 45 300'
          - --segmentation ilastik,mesmer
          - --segmentation cellpose --mcquant-opts '--masks *masks.tif'
          - --viz --segmentation ilastik -profile singularity
    needs: setup
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Install Singularity
        uses: eWaterCycle/setup-singularity@v7
        if: ${{ contains(matrix.params, 'singularity') }}
        with:
          singularity-version: 3.8.3
      - name: Install Nextflow
        run: curl -fsSL get.nextflow.io | bash
      - name: Restore exemplar-001 cache
        uses: actions/cache@v3
        if: ${{ !contains(matrix.params, 'background') }}
        with:
          path: ~/data/exemplar-001
          key: ex001-2022-02-24
      - name: Restore exemplar-001 (w/ autofluorescence) cache
        uses: actions/cache@v3
        if: ${{ contains(matrix.params, 'background') }}
        with:
          path: ~/data/af/exemplar-001
          key: ex001-af-2023-01-14
      - name: Adjust data location for the autofluorescence exemplar
        if: ${{ contains(matrix.params, 'background') }}
        run: mv ~/data/af/exemplar-001 ~/data
      - name: Test exemplar-001 with additional parameters
        run: |
          docker rmi -f $(docker images -a -q)
          ./nextflow main.nf --in ~/data/exemplar-001 ${{ matrix.params }}
          ls -R ~/data/exemplar-001
      - name: Upload processed result
        uses: actions/upload-artifact@v4
        if: ${{ github.event_name == 'push' && contains(matrix.params, 'viz') }}
        with:
          name: exemplar-001
          path: |
            ~/data/exemplar-001
            !~/data/exemplar-001/raw
            !~/data/exemplar-001/illumination
  
  # Step-by-step test of exemplar-001
  ex001-by-step:
    needs: setup
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Install Nextflow
        run: curl -fsSL get.nextflow.io | bash
      - name: Restore exemplar-001 cache
        uses: actions/cache@v3
        with:
          path: ~/data/exemplar-001
          key: ex001-2022-02-24
      - name: Test exemplar-001 step-by-step
        run: |
          docker rmi -f $(docker images -a -q)
          ./nextflow main.nf --in ~/data/exemplar-001 --start-at registration --stop-at registration
          ./nextflow clean -f last
          ./nextflow main.nf --in ~/data/exemplar-001 --start-at segmentation --stop-at segmentation
          ./nextflow main.nf --in ~/data/exemplar-001 --start-at watershed --stop-at watershed
          ./nextflow main.nf --in ~/data/exemplar-001 --start-at quantification --stop-at quantification
          docker rmi -f $(docker images -a -q)
          ./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream scimap
          ./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream naivestates
          ./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream fastpg
          ./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream scanpy
          ./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream flowsom
          ls -R ~/data/exemplar-001

  # One-shot test of exemplar-002
  ex002:
    needs: setup
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Install Nextflow
        run: curl -fsSL get.nextflow.io | bash
      - name: Restore exemplar-002 cache
        uses: actions/cache@v3
        with:
          path: ~/data/exemplar-002
          key: ex002-2022-02-24
      - name: Test exemplar-002
        run: |
          docker rmi -f $(docker images -a -q)
          ./nextflow main.nf --in ~/data/exemplar-002 --tma --start-at registration --stop-at segmentation
          docker rmi -f $(docker images -a -q)
          ./nextflow main.nf --in ~/data/exemplar-002 --tma --start-at quantification
          ls -R ~/data/exemplar-002