Fix ci #19
Workflow file for this run
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name: Run basic tests for Lemur | |
on: | |
push: | |
branches: [ "main" ] | |
pull_request: | |
branches: [ "main" ] | |
jobs: | |
test: | |
name: Test Lemur executable | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
shell: bash -l {0} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest, macos-13] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Setup Miniconda | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
environment-file: ./lemur.yml | |
activate-environment: lemur-env | |
python-version: 3.9 | |
- name: Create output folder | |
run: | | |
mkdir ./examples/example-output | |
- name: Run Lemur | |
run: ./lemur -i ./examples/example-data/example.fastq | |
-o ./examples/example-output | |
-d ./examples/example-db | |
--tax-path ./examples/example-db/taxonomy.tsv | |
-r species | |
--verbose; | |
- name: Check that output was produced | |
id: check_files | |
uses: andstor/[email protected] | |
with: | |
files: "./examples/example-output/P_rgs_df.tsv, ./examples/example-output/relative_abundance.tsv, ./examples/example-output/relative_abundance-species.tsv" | |
fail: true | |
- name: Check if outputed profile matches reference | |
uses: LouisBrunner/[email protected] | |
with: | |
old: ./examples/example-output-ref/relative_abundance.tsv | |
new: ./examples/example-output/relative_abundance.tsv | |
mode: strict | |
tolerance: same | |
output: ./examples/example-output/relative_abundance_diff.txt | |
- name: Archive production artifacts | |
uses: actions/upload-artifact@v3 | |
with: | |
name: lemur-out-log | |
path: ./examples/example-output/* | |
retention-days: 5 |