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Add AWS megatest GHA #154

Merged
merged 14 commits into from
Mar 12, 2020
Merged

Add AWS megatest GHA #154

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c7aea97
Set up GHA to install awscli with conda
FriederikeHanssen Mar 5, 2020
dcab941
Update naming
FriederikeHanssen Mar 5, 2020
4ffb22c
Update naming
FriederikeHanssen Mar 5, 2020
e4fb71a
Add variables for access tokens
FriederikeHanssen Mar 11, 2020
717da50
Test awscli install separatly
FriederikeHanssen Mar 11, 2020
8aa31bb
Add with: keyword
FriederikeHanssen Mar 11, 2020
3f52dee
Change action to goanpeca and test aws install
FriederikeHanssen Mar 11, 2020
a8a19e4
Add aws run back in
FriederikeHanssen Mar 11, 2020
58200c2
set to only be run on PR to master or release
FriederikeHanssen Mar 11, 2020
17df486
Merge branch 'dev' into aws_megatests2
maxulysse Mar 11, 2020
ce7f2ba
Merge remote-tracking branch 'upstream/dev' into aws_megatests2
FriederikeHanssen Mar 11, 2020
676ead5
Merge branch 'aws_megatests2' of https://github.com/friederikehanssen…
FriederikeHanssen Mar 11, 2020
0f51322
Move changes from aws.yml to awstest.yml
FriederikeHanssen Mar 11, 2020
f1c1415
Add nextflow tower properly as suggested
FriederikeHanssen Mar 11, 2020
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43 changes: 21 additions & 22 deletions .github/workflows/awstest.yml
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Original file line number Diff line number Diff line change
@@ -1,31 +1,30 @@
name: nf-core aws test
name: AWS Megatests
# This workflow is triggered on PRs to the master branch.
# It runs the -profile 'test' on AWS batch

on:
pull_request:
branches:
- master
- 'master'
release:
types: [published]

jobs:
Awstest:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ['ubuntu-latest']
python-version: ['3.7']
steps:
- uses: goanpeca/setup-miniconda@v1
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
- name: Install aws client
run: conda install -c conda-forge awscli
- name: Start AWS batch job
env:
AWS_ACCESS_KEY_ID: ${{secrets.AWS_KEY_ID}}
AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_KEY_SECRET}}
TOWER_ACCESS_TOKEN: ${{secrets.TOWER_ACCESS_TOKEN}}
run: |
aws batch submit-job --region eu-west-1 --job-name nf-core-sarek --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' --job-definition nextflow --container-overrides command=nf-core/sarek,"-r ${GITHUB_SHA} -profile test --outdir s3://nf-core-awsmegatests/sarek/results-${GITHUB_SHA} -w s3://nf-core-awsmegatests/sarek/work-${GITHUB_SHA}"
run-awstest:
name: Run AWS test
runs-on: ubuntu-latest
steps:
- name: Setup Miniconda
uses: goanpeca/setup-miniconda@v1.0.2
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_KEY_ID}}
AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_KEY_SECRET}}
TOWER_ACCESS_TOKEN: ${{secrets.TOWER_ACCESS_TOKEN}}
run: |
aws batch submit-job --region eu-west-1 --job-name nf-core-sarek --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' --job-definition nextflow --container-overrides command=nf-core/sarek,"-r ${GITHUB_SHA} -profile test --outdir s3://nf-core-awsmegatests/sarek/results-${GITHUB_SHA} -w s3://nf-core-awsmegatests/sarek/work-${GITHUB_SHA}"