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Allow tarballed inputs instead of only directories #149

Allow tarballed inputs instead of only directories

Allow tarballed inputs instead of only directories #149

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:
- dev
pull_request:
branches:
- dev
- master
release:
types: [published]
env:
NXF_ANSI_LOG: false
CAPSULE_LOG: none
NFTEST_VER: "0.7.3"
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
define_nxf_versions:
name: Choose nextflow versions to test against depending on target branch
runs-on: ubuntu-latest
outputs:
matrix: ${{ steps.nxf_versions.outputs.matrix }}
steps:
- id: nxf_versions
run: |
if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
else
echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT
fi
test:
name: Run pipeline with test data
needs: define_nxf_versions
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
test:
- tests/pipeline/test_spaceranger_ffpe_v1.nf.test
- tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test
- tests/pipeline/test_downstream.nf.test
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Checkout test data
uses: actions/checkout@v3
with:
repository: nf-core/test-datasets
ref: spatialtranscriptomics
fetch-depth: 1
path: test-datasets
# Install Nextflow
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
# Install nf-test
- name: Install nf-test
run: |
wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
sudo mv nf-test /usr/local/bin/
# Run nf-test
- name: Run nf-test
run: nf-test test --profile=test,docker --tap=test.tap ${{ matrix.test }}
# If the test fails, output the software_versions.yml using the 'batcat' utility
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always .nf-test/tests/*/output/pipeline_info/software_versions.yml