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Merge pull request #1160 from drpatelh/fixes
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Final prerelease fixes to fix Cloud CI
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drpatelh authored Jan 8, 2024
2 parents 805c5ac + 36c89c1 commit eb5392a
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36 changes: 18 additions & 18 deletions .github/workflows/cloud_tests_full.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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: |
{
Expand All @@ -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:
Expand Down
29 changes: 17 additions & 12 deletions .github/workflows/cloud_tests_small.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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: |
{
Expand All @@ -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:
Expand Down
4 changes: 3 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -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
Expand Down
2 changes: 1 addition & 1 deletion nextflow_schema.json
Original file line number Diff line number Diff line change
Expand Up @@ -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."
Expand Down

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