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Merge pull request #126 from nf-core/dev
Dev > Master for 1.1.0 release
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name: nf-core AWS full test | ||
# This workflow is triggered on releases. | ||
# It runs the -profile 'test_full' on AWS batch | ||
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on: | ||
release: | ||
types: [published] | ||
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jobs: | ||
run-awstest: | ||
if: github.repository == 'nf-core/viralrecon' | ||
name: Run AWS test | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Setup Miniconda | ||
uses: goanpeca/[email protected] | ||
with: | ||
auto-update-conda: true | ||
python-version: 3.7 | ||
- name: Install awscli | ||
run: conda install -c conda-forge awscli | ||
- name: Start AWS batch job | ||
env: | ||
AWS_ACCESS_KEY_ID: ${{secrets.AWS_ACCESS_KEY_ID}} | ||
AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_SECRET_ACCESS_KEY}} | ||
TOWER_ACCESS_TOKEN: ${{secrets.AWS_TOWER_TOKEN}} | ||
#AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}} | ||
AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}} | ||
AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}} | ||
run: | # Submits job to AWS batch using a 'nextflow-4GiB' job definition. Setting JVM options to "-XX:+UseG1GC" for more efficient garbage collection when staging remote files. | ||
aws batch submit-job \ | ||
--region eu-west-1 \ | ||
--job-name nf-core-viralrecon \ | ||
--job-queue $AWS_JOB_QUEUE \ | ||
--job-definition nextflow-4GiB \ | ||
--container-overrides '{"command": ["nf-core/viralrecon", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/viralrecon/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/viralrecon/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}' |
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name: nf-core branch protection | ||
# This workflow is triggered on PRs to master branch on the repository | ||
# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` | ||
on: | ||
pull_request: | ||
branches: | ||
- master | ||
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jobs: | ||
test: | ||
runs-on: ubuntu-18.04 | ||
steps: | ||
# PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch | ||
- name: Check PRs | ||
run: | | ||
{ [[ $(git remote get-url origin) == *nf-core/viralrecon ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]] | ||
name: nf-core branch protection | ||
# This workflow is triggered on PRs to master branch on the repository | ||
# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` | ||
on: | ||
pull_request: | ||
branches: | ||
- master | ||
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||
jobs: | ||
test: | ||
runs-on: ubuntu-18.04 | ||
steps: | ||
# PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch | ||
- name: Check PRs | ||
run: | | ||
{ [[ $(git remote get-url origin) == *nf-core/viralrecon ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]] |
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name: nf-core CI | ||
# This workflow is triggered on pushes and PRs to the repository. | ||
# This workflow is triggered on releases and pull-requests. | ||
# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
on: [push, pull_request] | ||
on: | ||
push: | ||
branches: | ||
- dev | ||
pull_request: | ||
release: | ||
types: [published] | ||
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||
jobs: | ||
test: | ||
name: Test default workflow | ||
# 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/viralrecon') }} | ||
runs-on: ubuntu-latest | ||
env: | ||
NXF_VER: ${{ matrix.nxf_ver }} | ||
NXF_ANSI_LOG: false | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
# Nextflow versions: check pipeline minimum and current latest | ||
nxf_ver: ['19.10.0', ''] | ||
steps: | ||
- uses: actions/checkout@v2 | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v2 | ||
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||
- 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/viralrecon:1.1.0 | ||
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- name: Pull docker image | ||
if: ${{ !env.GIT_DIFF }} | ||
run: | | ||
docker pull nfcore/viralrecon:dev | ||
docker tag nfcore/viralrecon:dev nfcore/viralrecon:1.1.0 | ||
- name: Install Nextflow | ||
run: | | ||
wget -qO- get.nextflow.io | bash | ||
sudo mv nextflow /usr/local/bin/ | ||
- name: Pull docker image | ||
run: | | ||
docker pull nfcore/viralrecon:dev | ||
docker tag nfcore/viralrecon:dev nfcore/viralrecon:1.0.0 | ||
- name: Run pipeline with test data | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test,docker | ||
parameters: | ||
name: Test workflow parameters | ||
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }} | ||
runs-on: ubuntu-latest | ||
env: | ||
NXF_VER: '19.10.0' | ||
NXF_ANSI_LOG: false | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
parameters: [--skip_adapter_trimming, --skip_markduplicates, --skip_variants, --skip_amplicon_trimming, --skip_kraken2, --skip_assembly] | ||
parameters: [--skip_adapter_trimming, --skip_markduplicates, --skip_variants, --skip_amplicon_trimming, --skip_kraken2, --skip_assembly, '--callers ivar --assemblers spades'] | ||
steps: | ||
- uses: actions/checkout@v2 | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v2 | ||
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||
- 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/viralrecon:1.1.0 | ||
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- name: Pull docker image | ||
if: ${{ !env.GIT_DIFF }} | ||
run: | | ||
docker pull nfcore/viralrecon:dev | ||
docker tag nfcore/viralrecon:dev nfcore/viralrecon:1.1.0 | ||
- name: Install Nextflow | ||
run: | | ||
wget -qO- get.nextflow.io | bash | ||
sudo mv nextflow /usr/local/bin/ | ||
- name: Pull docker image | ||
run: | | ||
docker pull nfcore/viralrecon:dev | ||
docker tag nfcore/viralrecon:dev nfcore/viralrecon:1.0.0 | ||
- name: Run pipeline with test amplicon data with various options | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} | ||
test_sra: | ||
env: | ||
NXF_VER: '19.10.0' | ||
NXF_ANSI_LOG: false | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
parameters: [--skip_sra, ''] | ||
steps: | ||
- uses: actions/checkout@v2 | ||
- name: Install Nextflow | ||
run: | | ||
wget -qO- get.nextflow.io | bash | ||
sudo mv nextflow /usr/local/bin/ | ||
- name: Pull docker image | ||
run: | | ||
docker pull nfcore/viralrecon:dev | ||
docker tag nfcore/viralrecon:dev nfcore/viralrecon:1.0.0 | ||
- name: Run pipeline with minimal data via SRA ids and various options | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test_sra,docker ${{ matrix.parameters }} | ||
name: Test SRA workflow | ||
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }} | ||
runs-on: ubuntu-latest | ||
env: | ||
NXF_VER: '19.10.0' | ||
NXF_ANSI_LOG: false | ||
strategy: | ||
matrix: | ||
parameters: [--skip_sra, ''] | ||
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/viralrecon:1.1.0 | ||
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- name: Pull docker image | ||
if: ${{ !env.GIT_DIFF }} | ||
run: | | ||
docker pull nfcore/viralrecon:dev | ||
docker tag nfcore/viralrecon:dev nfcore/viralrecon:1.1.0 | ||
- name: Install Nextflow | ||
run: | | ||
wget -qO- get.nextflow.io | bash | ||
sudo mv nextflow /usr/local/bin/ | ||
- name: Run pipeline with minimal data via SRA ids and various options | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test_sra,docker ${{ matrix.parameters }} | ||
test_sispa: | ||
env: | ||
NXF_VER: '19.10.0' | ||
NXF_ANSI_LOG: false | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
parameters: [--gff false, ''] | ||
steps: | ||
- uses: actions/checkout@v2 | ||
- name: Install Nextflow | ||
run: | | ||
wget -qO- get.nextflow.io | bash | ||
sudo mv nextflow /usr/local/bin/ | ||
- name: Pull docker image | ||
run: | | ||
docker pull nfcore/viralrecon:dev | ||
docker tag nfcore/viralrecon:dev nfcore/viralrecon:1.0.0 | ||
- name: Run pipeline with minimal SISPA data and various options | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }} | ||
name: Test SISPA workflow | ||
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }} | ||
runs-on: ubuntu-latest | ||
env: | ||
NXF_VER: '19.10.0' | ||
NXF_ANSI_LOG: false | ||
strategy: | ||
matrix: | ||
parameters: [--gff false, ''] | ||
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/viralrecon:1.1.0 | ||
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||
- name: Pull docker image | ||
if: ${{ !env.GIT_DIFF }} | ||
run: | | ||
docker pull nfcore/viralrecon:dev | ||
docker tag nfcore/viralrecon:dev nfcore/viralrecon:1.1.0 | ||
- name: Install Nextflow | ||
run: | | ||
wget -qO- get.nextflow.io | bash | ||
sudo mv nextflow /usr/local/bin/ | ||
- name: Run pipeline with minimal SISPA data and various options | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }} | ||
push_dockerhub: | ||
name: Push new Docker image to Docker Hub | ||
runs-on: ubuntu-latest | ||
# Only run if the tests passed | ||
needs: test | ||
# Only run for the nf-core repo, for releases and merged PRs | ||
if: ${{ github.repository == 'nf-core/viralrecon' && (github.event_name == 'release' || github.event_name == 'push') }} | ||
env: | ||
DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }} | ||
DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }} | ||
steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v2 | ||
|
||
- name: Build new docker image | ||
run: docker build --no-cache . -t nfcore/viralrecon:latest | ||
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- name: Push Docker image to DockerHub (dev) | ||
if: ${{ github.event_name == 'push' }} | ||
run: | | ||
echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin | ||
docker tag nfcore/viralrecon:latest nfcore/viralrecon:dev | ||
docker push nfcore/viralrecon:dev | ||
- name: Push Docker image to DockerHub (release) | ||
if: ${{ github.event_name == 'release' }} | ||
run: | | ||
echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin | ||
docker push nfcore/viralrecon:latest | ||
docker tag nfcore/viralrecon:latest nfcore/viralrecon:${{ github.ref }} | ||
docker push nfcore/viralrecon:${{ github.ref }} |
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