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feat: Add entry to download references #101

feat: Add entry to download references

feat: Add entry to download references #101

Workflow file for this run

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
push:
branches:
- main
pull_request:
release:
types: [published]
env:
NXF_ANSI_LOG: false
jobs:
# test-stub:
# name: Run pipeline with stubs
# if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'beiko-lab/arete') }}"
# runs-on: ubuntu-latest
# strategy:
# matrix:
# NXF_VER:
# - "latest-everything"
# steps:
# - name: Check out pipeline code
# uses: actions/checkout@v2
# - name: Install Nextflow
# uses: nf-core/setup-nextflow@v1
# with:
# version: "${{ matrix.NXF_VER }}"
# - name: Run pipeline stub-run
# run: |
# nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub-run --outdir ./stub_results
test:
name: Run pipeline with test data
runs-on: ubuntu-latest
strategy:
matrix:
profile: ["docker", "singularity"]
NXF_VER:
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Set up Singularity
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5
with:
singularity-version: 3.7.1
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} --outdir ./results