diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml new file mode 100644 index 00000000..15f940dd --- /dev/null +++ b/.github/workflows/awsfulltest.yml @@ -0,0 +1,36 @@ +name: nf-core AWS full size tests +# This workflow is triggered on releases. +# It runs the -profile 'test_full' on AWS batch + +on: + release: + types: [published] + +jobs: + run-awstest: + if: github.repository == 'nf-core/atacseq' + 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_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-atacseq \ + --job-queue $AWS_JOB_QUEUE \ + --job-definition nextflow-4GiB \ + --container-overrides '{"command": ["nf-core/atacseq", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/atacseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/atacseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}' diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index c315d213..fae13576 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -1,37 +1,38 @@ -name: nf-core AWS test -# This workflow is triggered on PRs to the master branch. -# It runs the -profile 'test_full' on AWS batch - -on: - push: - branches: - - master - - dev - release: - types: [published] - -jobs: - run-awstest: - if: github.repository == 'nf-core/atacseq' - 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: ${{secrets.TOWER_ACCESS_TOKEN}} - run: | # Submits job to AWS batch using a 'nextflow-4GiB' instance. Setting JVM options to "-XX:+UseG1GC" for more efficient garbage collection when staging remote files. - aws batch submit-job \ - --region eu-west-1 \ - --job-name nf-core-atacseq \ - --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' \ - --job-definition nextflow-4GiB \ - --container-overrides '{"command": ["nf-core/atacseq", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://nf-core-awsmegatests/atacseq/results-'"${GITHUB_SHA}"' -w s3://nf-core-awsmegatests/atacseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}' +name: nf-core AWS test +# This workflow is triggered on push to the master branch. +# It runs the -profile 'test' on AWS batch + +on: + push: + branches: + - master + - dev # just for testing purposes, to be removed + +jobs: + run-awstest: + if: github.repository == 'nf-core/atacseq' + 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_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-atacseq \ + --job-queue $AWS_JOB_QUEUE \ + --job-definition nextflow-4GiB \ + --container-overrides '{"command": ["nf-core/atacseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/atacseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/atacseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}' diff --git a/CHANGELOG.md b/CHANGELOG.md index 7d4aba66..1a13e46e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * [nf-core/chipseq#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system * [nf-core/chipseq#154](https://github.com/nf-core/chipseq/issues/154) - computeMatrix.val.mat.gz files not zipped * Make executables in `bin/` compatible with Python 3 +* [#110](https://github.com/nf-core/atacseq/pull/110) - updated AWS test GitHub actions ### `Dependencies`