.gitlab-ci.yml

image: openjdk:11.0.10-jre-buster

before_script:
  - java -version
  - apt-get update && apt-get --assume-yes install wget make procps
  - wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow
  - nextflow help
  - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  - mkdir /root/.conda
  - bash Miniconda3-latest-Linux-x86_64.sh -b && cp /root/miniconda3/bin/* /usr/local/bin/
  - rm -f Miniconda3-latest-Linux-x86_64.sh
  - conda --version
  - conda env create -f environment.yml --name bam2tensor_env
  - conda init bash
  - source ~/.bashrc
  - conda activate bam2tensor_env


test_aligner:
  script:
    - python tests/test_aligner.py

test_aligner_utils:
  script:
    - python tests/test_aligner_utils.py

test_intermediate_matrices:
  script:
    - python tests/test_intermediary_matrices.py

#stages:
#  - test
#
#test:
#  stage: test
#  script:
#    - make