From 36c89c1f1bd523820deb9a1363a6e9c52d3fc8b7 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 8 Jan 2024 15:01:52 +0000 Subject: [PATCH] Final prerelease fixes --- .github/workflows/cloud_tests_full.yml | 36 ++++++++++++------------- .github/workflows/cloud_tests_small.yml | 29 +++++++++++--------- CHANGELOG.md | 4 ++- nextflow_schema.json | 2 +- 4 files changed, 39 insertions(+), 32 deletions(-) diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml index 0396119f6..c7ba753bb 100644 --- a/.github/workflows/cloud_tests_full.yml +++ b/.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: | { @@ -43,8 +43,8 @@ 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: @@ -52,26 +52,27 @@ 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: ${{ secrets.TOWER_CE_GCP_CPU }} - workdir: "${{ 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: @@ -79,19 +80,18 @@ 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: ${{ secrets.TOWER_CE_AZURE_CPU }} - workdir: "${{ 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: diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml index 0fe3cddd1..69647ff04 100644 --- a/.github/workflows/cloud_tests_small.yml +++ b/.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: diff --git a/CHANGELOG.md b/CHANGELOG.md index 7f66ad420..e2d4c8fc8 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/nextflow_schema.json b/nextflow_schema.json index 36ba670c9..42e4e8967 100644 --- a/nextflow_schema.json +++ b/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."