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ci.yml
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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:
release:
types: [published]
jobs:
test:
name: Run workflow tests
# Only run on push if this is the nf-core dev branch (merged PRs)
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
strategy:
matrix:
# Nextflow versions: check pipeline minimum and current latest
nxf_ver: ['19.10.0', '']
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Check if Dockerfile or Conda environment changed
uses: technote-space/get-diff-action@v1
with:
PREFIX_FILTER: |
Dockerfile
environment.yml
- name: Build new docker image
if: env.GIT_DIFF
run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
- name: Pull docker image
if: ${{ !env.GIT_DIFF }}
run: |
docker pull nfcore/nanoseq:dev
docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker
profile:
name: Run profile tests
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
runs-on: ubuntu-latest
env:
NXF_VER: '19.10.0'
NXF_ANSI_LOG: false
strategy:
matrix:
profiles: [test_bc_nodx, test_nobc_dx, test_nobc_nodx, test_nobc_nodx_noaln]
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Check if Dockerfile or Conda environment changed
uses: technote-space/get-diff-action@v1
with:
PREFIX_FILTER: |
Dockerfile
environment.yml
- name: Build new docker image
if: env.GIT_DIFF
run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
- name: Pull docker image
if: ${{ !env.GIT_DIFF }}
run: |
docker pull nfcore/nanoseq:dev
docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run pipeline with different profiles
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profiles }},docker
parameters:
name: Run parameter tests
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
runs-on: ubuntu-latest
env:
NXF_VER: '19.10.0'
NXF_ANSI_LOG: false
strategy:
matrix:
parameters: [--aligner graphmap2, --skip_alignment, --skip_qc, --skip_quantification]
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Check if Dockerfile or Conda environment changed
uses: technote-space/get-diff-action@v1
with:
PREFIX_FILTER: |
Dockerfile
environment.yml
- name: Build new docker image
if: env.GIT_DIFF
run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
- name: Pull docker image
if: ${{ !env.GIT_DIFF }}
run: |
docker pull nfcore/nanoseq:dev
docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run pipeline with different parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
quantification:
name: Run quantification tests
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
runs-on: ubuntu-latest
env:
NXF_VER: '19.10.0'
NXF_ANSI_LOG: false
strategy:
matrix:
parameters: [--quantification_method 'stringtie2', --skip_quantification, --skip_differential_analysis]
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Check if Dockerfile or Conda environment changed
uses: technote-space/get-diff-action@v1
with:
PREFIX_FILTER: |
Dockerfile
environment.yml
- name: Build new docker image
if: env.GIT_DIFF
run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
- name: Pull docker image
if: ${{ !env.GIT_DIFF }}
run: |
docker pull nfcore/nanoseq:dev
docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run pipeline with different quantification parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_nobc_nodx,docker ${{ matrix.parameters }}