Merge pull request #110 from ggabernet/dev

Update aws test GitHub Actions
nf-core · Jun 30, 2020 · 9245dbf · 9245dbf
2 parents 12b8d0b + 074bb15
commit 9245dbf
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diff --git a/.github/workflows/awsfulltest.yml 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
@@ -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
@@ -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`