latest-dry-run #28
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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: "<2" | |
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 --help | |
./comparem2 --version | |
./comparem2 --cite | |
./comparem2 --status | |
- name: dry run | |
run: | | |
./comparem2 --dry-run | |
rm -rf .snakemake results_comparem2 | |
./comparem2 --until metadata | |
rm -rf .snakemake results_comparem2 | |
touch dummy_1.fa; ./comparem2 --dry-run | |
touch dummy_2.fa; ./comparem2 --dry-run | |
touch dummy_3.fa; ./comparem2 --dry-run | |
unzip tests/E._faecium/fna.zip | |
./comparem2 --config input_genomes="*.fna" --dry-run | |
./comparem2 --config input_genomes="*.fna" --until fast --dry-run | |
./comparem2 --config input_genomes="*.fna" --until isolate --dry-run | |
./comparem2 --config input_genomes="*.fna" --until meta --dry-run | |
./comparem2 --config input_genomes="*.fna" --until downloads --dry-run | |
ls dummy_{2,3}.fa > fofn.txt; ./comparem2 --config fofn="fofn.txt" --dry-run | |