Final prerelease fixes to fix Cloud CI

.github/workflows/cloud_tests_full.yml

@@ -25,12 +25,12 @@ jobs:
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
-          revision: ${{ github.sha }}
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
           run_name: "aws_rnaseq_full_${{ matrix.aligner }}"
+          revision: ${{ github.sha }}
           profiles: test_full_aws
           parameters: |
             {
@@ -43,55 +43,55 @@ jobs:
           name: Tower debug log file
           path: tower_action_*.log
 
-  run-full-tests-on-gcp:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }}
+  run-full-tests-on-azure:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
         aligner: ["star_salmon", "star_rsem"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
-          revision: ${{ github.sha }}
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
-          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
-          run_name: "gcp_rnaseq_full_${{ matrix.aligner }}"
-          profiles: test_full_gcp
+          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
+          run_name: "azure_rnaseq_full_${{ matrix.aligner }}"
+          revision: ${{ github.sha }}
+          profiles: test_full_azure
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
                 "aligner": "${{ matrix.aligner }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
+                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/",
+                "igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
             }
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
           path: tower_action_*.log
 
-  run-full-tests-on-azure:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
+  run-full-tests-on-gcp:
+    if: ${{ github.event.inputs.platform == 'gcp' || !github.event.inputs }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
         aligner: ["star_salmon", "star_rsem"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
-          revision: ${{ github.sha }}
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
-          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
-          run_name: "azure_rnaseq_full_${{ matrix.aligner }}"
-          profiles: test_full_azure
+          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
+          run_name: "gcp_rnaseq_full_${{ matrix.aligner }}"
+          revision: ${{ github.sha }}
+          profiles: test_full_gcp
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
                 "aligner": "${{ matrix.aligner }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/",
-                "igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
+                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
             }
       - uses: actions/upload-artifact@v3
         with:

.github/workflows/cloud_tests_small.yml

@@ -25,6 +25,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
           run_name: "aws_rnaseq_small"
+          revision: ${{ github.sha }}
           profiles: test
           parameters: |
             {
@@ -34,41 +35,45 @@ jobs:
         with:
           name: Tower debug log file
           path: tower_action_*.log
-  run-small-tests-on-gcp:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
+
+  run-small-tests-on-azure:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
     runs-on: ubuntu-latest
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
-          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
-          run_name: "gcp_rnaseq_small"
+          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
+          run_name: "azure_rnaseq_small"
+          revision: ${{ github.sha }}
           profiles: test
           parameters: |
             {
-                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}/"
+                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
           path: tower_action_*.log
-  run-small-tests-on-azure:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
+
+  run-small-tests-on-gcp:
+    if: ${{ github.event.inputs.platform == 'gcp' }}
     runs-on: ubuntu-latest
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
-          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
-          run_name: "azure_rnaseq_small"
+          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
+          run_name: "gcp_rnaseq_small"
+          revision: ${{ github.sha }}
           profiles: test
           parameters: |
             {
-                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}/"
+                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}/"
             }
       - uses: actions/upload-artifact@v3
         with:

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v3.14.0 - 2024-01-08
+## [[3.14.0](https://github.com/nf-core/rnaseq/releases/tag/3.14.0)] - 2024-01-08
 
 ### Credits
 
@@ -17,6 +17,8 @@ Special thanks to the following for their contributions to the release:
 - [Phil Ewels](https://github.com/ewels)
 - [Vlad Savelyev](https://github.com/vladsavelyev)
 
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
 ### Enhancements & fixes
 
 - [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling

nextflow_schema.json

@@ -403,7 +403,7 @@
                 },
                 "min_mapped_reads": {
                     "type": "number",
-                    "default": 5,
+                    "default": 5.0,
                     "fa_icon": "fas fa-percentage",
                     "description": "Minimum percentage of uniquely mapped reads below which samples are removed from further processing.",
                     "help_text": "Some downstream steps in the pipeline will fail if this threshold is too low."