Merge pull request #777 from FriederikeHanssen/aws_paths

AWS outdir paths were mixed up
nf-core · Oct 10, 2022 · 9b40b12 · 9b40b12
2 parents 668893f + c96e13e
commit 9b40b12
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diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -20,10 +20,10 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/germline_test
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/somatic_test
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test"
             }
           profiles: test_full,aws_tower
       - uses: actions/upload-artifact@v3

diff --git a/.github/workflows/awsfulltest_somatic.yml → .github/workflows/awsfulltest_germline.yml b/.github/workflows/awsfulltest_somatic.yml → .github/workflows/awsfulltest_germline.yml
@@ -20,9 +20,9 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/somatic_test
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/germline_test
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test"
             }
           profiles: test_full_somatic,aws_tower
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#768](https://github.com/nf-core/sarek/pull/768) - Use double quotes to fix import of singularity images for deepvariant module
 - [#770](https://github.com/nf-core/sarek/pull/770) - Use double quotes to fix import of singularity images for gatk4/cnnscorevariants module
 - [#771](https://github.com/nf-core/sarek/pull/771) - update to new modules syntax
+- [#777](https://github.com/nf-core/sarek/pull/777) - Fix mixed up aws full size tests output paths
 
 ### Deprecated