Merge branch 'dev' into dev

.github/workflows/awstest.yml

@@ -0,0 +1,30 @@
+name: nf-core aws test
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the -profile 'test' on AWS batch
+on:
+  push:
+  pull_request:
+  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,"-profile test --out_dir s3://nf-core-awsmegatests/sarek/results -w s3://nf-core-awsmegatests/sarek/work"

CHANGELOG.md

@@ -13,6 +13,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#115](https://github.com/nf-core/sarek/pull/115) - Add [@szilvajuhos](https://github.com/szilvajuhos) abstract for ESHG2020
 - [#117](https://github.com/nf-core/sarek/pull/117) - Add `Trim Galore` possibilities to Sarek
 - [#141](https://github.com/nf-core/sarek/pull/141) - Add containers for `WBcel235`
+- GitHub actions AWS megatests
 
 ### `Changed`