.gitlab-ci.yml

include:
    - project: "epi2melabs/ci-templates"
      file: "wf-containers.yaml"

variables:
    NF_WORKFLOW_OPTS: "--fastq test_data/fastq --sample_sheet test_data/sample_sheet.csv"
    NF_IGNORE_PROCESSES: "checkSampleSheet,combineGenotypeSummaries,genotypeSummary,report_no_data"
    CI_FLAVOUR: "new"


docker-run:
    artifacts:
        when: always
        exclude:
          - ${CI_PROJECT_NAME}/workspace/**/*
    parallel:
        matrix:
            - MATRIX_NAME: [
                "Midnight-ONT/V1",
                "Midnight-ONT/V2",
                "ARTIC/V4.1",
                "ARTIC/V5.3.2",
                "Midnight-IDT/V2",
                "NEB-VarSkip/v2",
                "no-basecall-model",
                "no-basecall-model-override-basecaller-cfg",
            ]
    rules:
        - if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
          when: never
        - if: $MATRIX_NAME == "Midnight-ONT/V1"
          variables:
              NF_WORKFLOW_OPTS: "--fastq test_data/fastq --sample_sheet test_data/sample_sheet.csv --scheme_name SARS-CoV-2 --scheme_version Midnight-ONT/V1"
        - if: $MATRIX_NAME == "Midnight-ONT/V2"
          variables:
              NF_WORKFLOW_OPTS: "--fastq test_data/fastq --sample_sheet test_data/sample_sheet.csv --scheme_name SARS-CoV-2 --scheme_version Midnight-ONT/V2"
        - if: $MATRIX_NAME == "ARTIC/V4.1"
          variables:
              NF_WORKFLOW_OPTS: "--fastq test_data/fastq --sample_sheet test_data/sample_sheet.csv --scheme_name SARS-CoV-2 --scheme_version ARTIC/V4.1"
        - if: $MATRIX_NAME == "ARTIC/V5.3.2"
          variables:
              NF_WORKFLOW_OPTS: "--fastq test_data/fastq --sample_sheet test_data/sample_sheet.csv --scheme_name SARS-CoV-2 --scheme_version ARTIC/V5.3.2"
        - if: $MATRIX_NAME == "Midnight-IDT/V2"
          variables:
              NF_WORKFLOW_OPTS: "--fastq test_data/fastq --sample_sheet test_data/sample_sheet.csv --scheme_name SARS-CoV-2 --scheme_version Midnight-IDT/V2"
        - if: $MATRIX_NAME == "NEB-VarSkip/v2"
          variables:
              NF_WORKFLOW_OPTS: "--fastq test_data/fastq --sample_sheet test_data/sample_sheet.csv --scheme_name SARS-CoV-2 --scheme_version NEB-VarSkip/v2"
        - if: $MATRIX_NAME == "no-basecall-model"
          variables:
            NF_WORKFLOW_OPTS: "--fastq test_data/fastq-no-basecall-model --scheme_name SARS-CoV-2 --scheme_version NEB-VarSkip/v2"
            ASSERT_NEXTFLOW_FAILURE: 1
            ASSERT_NEXTFLOW_FAILURE_REXP: Found no basecall model information in the input data for sample .*\. Please provide it with the `--override_basecaller_cfg` parameter.
        - if: $MATRIX_NAME == "no-basecall-model-override-basecaller-cfg"
          variables:
            NF_WORKFLOW_OPTS: "--fastq test_data/fastq-no-basecall-model --scheme_name SARS-CoV-2 --scheme_version NEB-VarSkip/v2 --override_basecaller_cfg dna_r9.4.1_e8_hac@v3.3"
            # the wf won't fail if artic fails; make sure we got a status of `1` in the consensus status file
            AFTER_NEXTFLOW_CMD: awk '$$1 == "barcode01" {if ($$2 != 1) exit 1}' $$PWD/$$CI_PROJECT_NAME/consensus_status.txt