# 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)
    NF_BEFORE_SCRIPT: |
       wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf  test_data.tar.gz
    NF_WORKFLOW_OPTS: "--fastq  ERR6053095_chr20.fastq \
      --ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
      --jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22"