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integration.yaml
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name: CI
on:
push:
branches:
- master
pull_request:
branches: [ master ]
workflow_dispatch:
jobs:
Testing_ASV:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: Test workflow
uses: snakemake/snakemake-github-action@v1.24.0
with:
directory: '.tests'
snakefile: 'workflow/Snakefile'
args: "-j 1 --use-conda --conda-cleanup-pkgs cache --conda-prefix envs --show-failed-logs --configfile .tests/config/config.yaml"
stagein: |
conda config --set channel_priority strict
- name: Archive logs on fail
if: ${{ failure() }}
uses: actions/upload-artifact@v2
with:
name: foodme-fail-asv
path: .tests/logs/
if-no-files-found: error
retention-days: 3
Testing_OTU:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: Test workflow
uses: snakemake/snakemake-github-action@v1.24.0
with:
directory: '.tests'
snakefile: 'workflow/Snakefile'
args: "-j 1 --use-conda --conda-cleanup-pkgs cache --conda-prefix envs --show-failed-logs --configfile .tests/config/config_otu.yaml"
stagein: |
conda config --set channel_priority strict
- name: Archive logs on fail
if: ${{ failure() }}
uses: actions/upload-artifact@v2
with:
name: foodme-fail-otu
path: .tests/logs/
if-no-files-found: error
retention-days: 3
Testing_benchmark:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: Test benchmark
uses: snakemake/snakemake-github-action@v1.23.0
with:
directory: '.tests'
snakefile: 'workflow/benchmark'
args: "-j 1 --use-conda --conda-cleanup-pkgs cache --conda-prefix envs --show-failed-logs --configfile .tests/config/config.yaml"
stagein: |
conda config --set channel_priority strict
- name: Archive logs on fail
if: ${{ failure() }}
uses: actions/upload-artifact@v2
with:
name: foodme-fail-benchmark
path: .tests/logs/
if-no-files-found: error
retention-days: 3
Testing_paramspace:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: Test workflow
uses: snakemake/snakemake-github-action@v1.24.0
with:
directory: '.tests'
snakefile: 'workflow/paramspace'
args: "-j 1 --use-conda --conda-cleanup-pkgs cache --conda-prefix envs --show-failed-logs --configfile .tests/config/config_paramspace.yaml"
stagein: |
conda config --set channel_priority strict
- name: Archive logs on fail
if: ${{ failure() }}
uses: actions/upload-artifact@v2
with:
name: foodme-fail-pspace
path: .tests/logs/
if-no-files-found: error
retention-days: 3