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dry-run.yaml
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name: latest-dry-run
on: workflow_dispatch
env:
COMPAREM2_PROFILE: "profile/conda/default"
jobs:
create-env:
name: ${{ matrix.os }}
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -l {0}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
steps:
- name: checkout repository
uses: actions/checkout@v2
- name: create environment with mamba
uses: conda-incubator/setup-miniconda@v2
with:
mamba-version: "*"
channels: conda-forge,bioconda,defaults
auto-activate-base: false
activate-environment: comparem2_launcher
environment-file: environment.yaml
- name: check solution
run: |
mamba env export
- name: test installation
run: |
python --version
snakemake --version
./comparem2 --version
./comparem2 --help
- name: dry run
run: |
unzip tests/E._faecium/fna.zip
./comparem2 --config input_genomes="*.fna" --dry-run