.gitlab-ci.yml

image: ubuntu:20.04

variables:
  GIT_SUBMODULE_STRATEGY: recursive

before_script:
  # install system dependencies
  - apt-get --quiet update && apt-get --quiet --assume-yes install curl unzip zip wget make tree
  # install SDKMAN as SDK version manager
  - curl -s "https://get.sdkman.io?rcupdate=false" | bash
  - source "/root/.sdkman/bin/sdkman-init.sh"
  - sdk version
  # install java (amazon coretto release 17.0.6)
  - sdk install java 17.0.6-amzn
  - java -version
  # install nextflow
  - wget -qO- https://get.nextflow.io | bash && mv nextflow /usr/local/bin/
  - which nextflow
  # install mamba
  - wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
  - mkdir /root/.conda
  - bash Mambaforge-Linux-x86_64.sh -b -p /usr/local/bin/conda
  - rm -f Mambaforge-Linux-x86_64.sh
  - source /usr/local/bin/conda/etc/profile.d/conda.sh
  - source /usr/local/bin/conda/etc/profile.d/mamba.sh
  - which mamba 
  - mamba --version
  # this is a workaround for https://github.com/mamba-org/mamba/issues/1993
  - echo "use_lockfiles:" >> ~/.condarc
  - echo "  - false" >> ~/.condarc
  - echo "channels:" >> ~/.condarc
  - echo "  - defaults" >> ~/.condarc
  - echo "  - conda-forge" >> ~/.condarc
  - echo "  - bioconda" >> ~/.condarc
  - cat ~/.condarc

stages:
  - Test

TEST-00:
  stage: Test
  script:
    - make clean test_00

TEST-01:
  stage: Test
  script:
    - make clean test_01

TEST-02:
  stage: Test
  script:
    - make clean test_02