Merge pull request #219 from ggabernet/awstest

update aws tests GitHub actions workflows

.github/workflows/awsfulltest.yml

@@ -0,0 +1,40 @@
+name: nf-core AWS test
+# This workflow is triggered on push to the master branch and on published releases.
+# It runs the -profile 'test' on AWS batch
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  run-awstest:
+    if: github.repository == 'nf-core/sarek'
+    name: Run AWS full tests
+    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
+        # TODO nf-core: You can customise AWS full pipeline tests as required
+        # Add full size test data (but still relatively small datasets for few samples) 
+        # on the `test_full.config` test runs with only one set of parameters
+        # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
+        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: |
+          aws batch submit-job \
+          --region eu-west-1 \
+          --job-name nf-core-sarek \
+          --job-queue $AWS_JOB_QUEUE \
+          --job-definition $AWS_JOB_DEFINITION \
+          --container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sarek/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/awstest.yml

@@ -6,8 +6,6 @@ on:
   push:
     branches:
       - master
-  release:
-    types: [published]
 
 jobs:
   run-awstest:
@@ -24,13 +22,16 @@ jobs:
         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}}
+          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: ${{secrets.AWS_S3_BUCKET}}
         run: |
           aws batch submit-job \
           --region eu-west-1 \
           --job-name nf-core-sarek \
-          --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' \
-          --job-definition nextflow \
-          --container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://nf-core-awsmegatests/sarek/results-'"${GITHUB_SHA}"' -w s3://nf-core-awsmegatests/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          --job-queue $AWS_JOB_QUEUE \
+          --job-definition $AWS_JOB_DEFINITION \
+          --container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sarek/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

CHANGELOG.md

@@ -13,6 +13,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#208](https://github.com/nf-core/sarek/pull/208) - Merge changes from the release PR
 - [#208](https://github.com/nf-core/sarek/pull/208) - Bump version to `3.0dev`
 - [#214](https://github.com/nf-core/sarek/pull/214) - Update `GATK` from `4.1.6.0` to `4.1.7.0`
+- [#219](https://github.com/nf-core/sarek/pull/219) - Added `awsfulltest.yml` GitHub Actions workflow
 
 ### Fixed
 
@@ -21,6 +22,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#214](https://github.com/nf-core/sarek/pull/214) - Fix channels collision between `Freebayes` and `Mutect2` [#200](https://github.com/nf-core/sarek/issues/200)
 - [#214](https://github.com/nf-core/sarek/pull/214) - Fix warning Invalid tag value for `CreateIntervalBeds` [#209](https://github.com/nf-core/sarek/issues/209)
 - [#214](https://github.com/nf-core/sarek/pull/214) - Fix `Mutect2` issue [#210](https://github.com/nf-core/sarek/issues/210)
+- [#219](https://github.com/nf-core/sarek/pull/219) - Updated awstest.yml GitHub actions workflow
 
 ### Deprecated