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Commit e62a936b authored by MihaelaZavolan's avatar MihaelaZavolan
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Use nextflow image in ci.yml

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image: python:3.9-slim-buster
stages: stages:
- qc - qc
- test - test
qc_1: qc_1:
stage: qc stage: qc
image: python:3.9-slim-buster
before_script: before_script:
- pip install -r requirements.txt - pip install -r requirements.txt
- pip install -r requirements_dev.txt - pip install -r requirements_dev.txt
- pip install -e . - pip install -e .
script: script:
- flake8 src/ setup.py - flake8 src/ setup.py
- coverage run --source src/ -m pytest - coverage run --source src/ -m pytest
...@@ -20,16 +17,7 @@ qc_1: ...@@ -20,16 +17,7 @@ qc_1:
test_1: test_1:
stage: test stage: test
image: nextflow/nexflow:21.10.3
before_script:
- pip install -r requirements.txt
- pip install -r requirements_dev.txt
- pip install -e .
- apt update -y
- apt install wget -y
- wget -qO- https://get.nextflow.io | bash
- nextflow self-update
script: script:
- nextflow main.nf - nextflow main.nf
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