Merge pull request #431 from ggabernet/dev

Update awstest GitHub actions workflow

.github/workflows/awstest.yml

@@ -25,13 +25,16 @@ 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.AWSTEST_KEY_ID}}
+          AWS_SECRET_ACCESS_KEY: ${{secrets.AWSTEST_KEY_SECRET}}
+          TOWER_ACCESS_TOKEN: ${{secrets.AWSTEST_TOWER_TOKEN}}
+          AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}}
+          AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}}
+          AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}}
         run: |
           aws batch submit-job \
             --region eu-west-1 \
             --job-name nf-core-rnaseq \
-            --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' \
-            --job-definition nextflow \
-            --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://nf-core-awsmegatests/rnaseq/results-'"${GITHUB_SHA}"' -w s3://nf-core-awsmegatests/rnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+            --job-queue $AWS_JOB_QUEUE \
+            --job-definition $AWS_JOB_DEFINITION \
+            --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

CHANGELOG.md

@@ -18,6 +18,7 @@
   * Pull-requests now rebuild the image if the software environment has been changed (so tests should pass)
   * Builds are done on GitHub Actions and pushed to Docker Hub, which is much faster than waiting for Docker Hub to build
 * Add option for `--additional_fasta` to provide ERCC spike-ins, transgenes such as GFP or CAR-T as additional sequences to align to [#419](https://github.com/nf-core/rnaseq/pull/419)
+* Updates awstest GitHub actions workflow with organization level secrets [#431](https://github.com/nf-core/rnaseq/pull/431/files)
 
 #### Updated Packages