.gitlab-ci.yml

# Include shared CI
include:
    - project: "epi2melabs/ci-templates"
      file: "wf-containers.yaml"

variables:
    # Workflow inputs given to nextflow.
    # The workflow should define `--out_dir`, the CI template sets this.
    # Only common file inputs and option values need to be given here
    # (not things such as -profile)
    CI_FLAVOUR: "new"
    NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/test_data.tar.gz  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-single-cell/v2.2.0_test_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ "
    NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB --threads 4 --fastq ${CI_PROJECT_NAME}/data/test_data/fastq/ --fastq_chunk 2500 --single_cell_sample_sheet ${CI_PROJECT_NAME}/data/test_data/samples.test.csv --ref_genome_dir ${CI_PROJECT_NAME}/data/test_data/refdata-gex-GRCh38-2020-A --matrix_min_genes 1 --matrix_min_cells 1 --matrix_max_mito 100"

docker-run:
    artifacts:
        when: always
        exclude: []

    parallel:
      matrix:
        - MATRIX_NAME: [
          "standard",
          "no_fl_filtering",
          "integration-test",
          "bam-input",
          "visium",

        ]
    rules:
      # NOTE As we're overriding the rules block for the included docker-run
      #   we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
      #   being incorrectly scheduled for "detached merge request pipelines" etc.
      - if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
        when: never
      - if: $MATRIX_NAME == 'standard'
        variables:
          NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/test_data.tar.gz  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-single-cell/v2.2.0_test_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/test_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
          NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB --threads 4 --fastq ${CI_PROJECT_NAME}/data/test_data/fastq/ --fastq_chunk 2500 --single_cell_sample_sheet ${CI_PROJECT_NAME}/data/test_data/samples.test.csv --ref_genome_dir ${CI_PROJECT_NAME}/data/test_data/refdata-gex-GRCh38-2020-A --matrix_min_genes 1 --matrix_min_cells 1 --matrix_max_mito 100"
      - if: $MATRIX_NAME == 'no_fl_filtering'
        variables:
          NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/test_data.tar.gz  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-single-cell/v2.2.0_test_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/test_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
          NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB --threads 4 --fastq ${CI_PROJECT_NAME}/data/test_data/fastq/ --fastq_chunk 2500 --full_length_only=false --single_cell_sample_sheet ${CI_PROJECT_NAME}/data/test_data/samples.test.csv --ref_genome_dir ${CI_PROJECT_NAME}/data/test_data/refdata-gex-GRCh38-2020-A --matrix_min_genes 1 --matrix_min_cells 1 --matrix_max_mito 100"

      - if: $MATRIX_NAME == "integration-test"
        variables:
          NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/ci_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-single-cell/ci_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/ci_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
          NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB --threads 4 --fastq ${CI_PROJECT_NAME}/data/ci_data/sample1.fq --fastq_chunk 2500 --ref_genome_dir ${CI_PROJECT_NAME}/data/ci_data/10x_ref_chr21_22 --matrix_min_genes 1 --matrix_min_cells 1 --expected_cells 10"
      - if: $MATRIX_NAME == "bam-input"
        variables:
          NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/test_data.tar.gz  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-single-cell/v2.2.0_test_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/test_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
          NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB --threads 4 --bam ${CI_PROJECT_NAME}/data/test_data/bam/ --fastq_chunk 2500 --single_cell_sample_sheet ${CI_PROJECT_NAME}/data/test_data/samples.test.csv --ref_genome_dir ${CI_PROJECT_NAME}/data/test_data/refdata-gex-GRCh38-2020-A --matrix_min_genes 1 --matrix_min_cells 1 --matrix_max_mito 100"
      - if: $MATRIX_NAME == "visium"
        variables:
          NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/test_data.tar.gz  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-single-cell/v2.2.0_test_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/test_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
          NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB --threads 4 --fastq ${CI_PROJECT_NAME}/data/test_data/visium_fastq --fastq_chunk 2500 --kit visium:v1 --ref_genome_dir ${CI_PROJECT_NAME}/data/test_data/refdata-gex-GRCm39-2024-A --matrix_min_genes 1 --matrix_min_cells 1 --matrix_max_mito 100"

macos-run:
  # Let's avoid those ARM64 runners for now
  tags:
    - macos
    - x86

integration_test:
  extends: .setup-alpine-nextflow
  dependencies: ["docker-run: [integration-test]"]
  stage: post-test
  script:
    - echo "ls" && ls
    - ls wf-single-cell
    - SHA=$(./nextflow config -properties|grep ${PYTEST_CONTAINER_CONFIG_KEY}|awk -F= '{print $2}')
    - IMAGE="${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:${SHA}"
    - docker run -u $(id -u) -v ${PWD}:/host $IMAGE pytest /host/test/workflow_integration.py;