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Merge pull request #221 from nf-core/dev
Dev -> Master for v2.2 release
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,43 +1,33 @@ | ||
name: nf-core AWS full size tests | ||
# This workflow is triggered on published releases. | ||
# It can be additionally triggered manually with GitHub actions workflow dispatch. | ||
# It can be additionally triggered manually with GitHub actions workflow dispatch button. | ||
# It runs the -profile 'test_full' on AWS batch | ||
|
||
on: | ||
release: | ||
types: [published] | ||
workflow_dispatch: | ||
|
||
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 }} | ||
|
||
jobs: | ||
run-awstest: | ||
run-tower: | ||
name: Run AWS full tests | ||
if: github.repository == 'nf-core/viralrecon' | ||
runs-on: ubuntu-latest | ||
# Do a full-scale run with data from each sequencing platform | ||
strategy: | ||
matrix: | ||
platform: ['illumina', 'nanopore'] | ||
platform: ["illumina", "nanopore"] | ||
steps: | ||
- name: Setup Miniconda | ||
uses: conda-incubator/setup-miniconda@v2 | ||
- name: Launch workflow via tower | ||
uses: nf-core/tower-action@master | ||
with: | ||
auto-update-conda: true | ||
python-version: 3.7 | ||
- name: Install awscli | ||
run: conda install -c conda-forge awscli | ||
- name: Start AWS batch job | ||
# Do a full-scale run with data from each sequencing platform | ||
run: | | ||
aws batch submit-job \ | ||
--region eu-west-1 \ | ||
--job-name nf-core-viralrecon \ | ||
--job-queue $AWS_JOB_QUEUE \ | ||
--job-definition $AWS_JOB_DEFINITION \ | ||
--container-overrides '{"command": ["nf-core/viralrecon", "-r '"${GITHUB_SHA}"' -profile test_full_'"${{matrix.platform}}"' --outdir s3://'"${AWS_S3_BUCKET}"'/viralrecon/results-'"${GITHUB_SHA}"'/platform_'"${{matrix.platform}}"' -w s3://'"${AWS_S3_BUCKET}"'/viralrecon/work-'"${GITHUB_SHA}"'/'"${{matrix.platform}}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' | ||
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }} | ||
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} | ||
pipeline: ${{ github.repository }} | ||
revision: ${{ github.sha }} | ||
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/viralrecon/work-${{ github.sha }} | ||
parameters: | | ||
{ | ||
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}/platform_${{ matrix.platform }}" | ||
} | ||
profiles: '[ "test_full_${{ matrix.platform }}", "aws_tower" ]' |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,37 +1,27 @@ | ||
name: nf-core AWS test | ||
# This workflow is triggered on push to the master branch. | ||
# It can be additionally triggered manually with GitHub actions workflow dispatch. | ||
# It runs the -profile 'test' on AWS batch. | ||
# This workflow can be triggered manually with the GitHub actions workflow dispatch button. | ||
# It runs the -profile 'test' on AWS batch | ||
|
||
on: | ||
workflow_dispatch: | ||
|
||
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 }} | ||
|
||
jobs: | ||
run-awstest: | ||
run-tower: | ||
name: Run AWS tests | ||
if: github.repository == 'nf-core/viralrecon' | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Setup Miniconda | ||
uses: conda-incubator/setup-miniconda@v2 | ||
- name: Launch workflow via tower | ||
uses: nf-core/tower-action@master | ||
|
||
with: | ||
auto-update-conda: true | ||
python-version: 3.7 | ||
- name: Install awscli | ||
run: conda install -c conda-forge awscli | ||
- name: Start AWS batch job | ||
run: | | ||
aws batch submit-job \ | ||
--region eu-west-1 \ | ||
--job-name nf-core-viralrecon \ | ||
--job-queue $AWS_JOB_QUEUE \ | ||
--job-definition $AWS_JOB_DEFINITION \ | ||
--container-overrides '{"command": ["nf-core/viralrecon", "-r '"${GITHUB_SHA}"' -profile test --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"'"}]}' | ||
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }} | ||
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} | ||
pipeline: ${{ github.repository }} | ||
revision: ${{ github.sha }} | ||
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/viralrecon/work-${{ github.sha }} | ||
parameters: | | ||
{ | ||
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}" | ||
} | ||
profiles: '[ "test", "aws_tower" ]' |
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Original file line number | Diff line number | Diff line change |
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|
@@ -3,7 +3,6 @@ work/ | |
data/ | ||
results/ | ||
.DS_Store | ||
tests/ | ||
testing/ | ||
testing* | ||
*.pyc |
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,6 @@ | ||
lint: | ||
files_unchanged: | ||
- .markdownlint.yml | ||
- assets/email_template.html | ||
- assets/email_template.txt | ||
- lib/NfcoreTemplate.groovy |
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