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Merge pull request #992 from nf-core/dev
Dev -> Master for v3.11.1 release
2 parents 48fb9b4 + 104ddaf commit 287afcf

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‎.github/workflows/ci.yml‎

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@@ -35,12 +35,17 @@ jobs:
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with:
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version: "${{ matrix.NXF_VER }}"
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: rnaseq3_10-test-data
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -65,7 +70,7 @@ jobs:
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star_salmon:
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name: Test STAR Salmon with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
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if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: rnaseq3_10-test-data
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -122,7 +132,7 @@ jobs:
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star_rsem:
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name: Test STAR RSEM with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
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if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: rnaseq3_10-test-data
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
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hisat2:
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name: Test HISAT2 with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
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if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: rnaseq3_10-test-data
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -214,7 +234,7 @@ jobs:
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salmon:
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name: Test Salmon with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
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if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: rnaseq3_10-test-data
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'

‎.github/workflows/cloud_tests_full.yml‎

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@@ -17,7 +17,7 @@ on:
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- gcp
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jobs:
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run-full-tests-on-aws:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"aligner": "${{ matrix.aligner }}",
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"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
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}
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wait: false
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: tower_action_*.log
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run-full-tests-on-gcp:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"aligner": "${{ matrix.aligner }}",
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"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
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}
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wait: false
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: tower_action_*.log
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run-full-tests-on-azure:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"aligner": "${{ matrix.aligner }}",
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"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
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"igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
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}
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wait: false
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file

‎.github/workflows/cloud_tests_small.yml‎

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{
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"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}"
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}
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wait: false
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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{
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"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}"
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}
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wait: false
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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{
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"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}"
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}
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wait: false
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file

‎CHANGELOG.md‎

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@@ -3,6 +3,24 @@
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [[3.11.1](https://github.com/nf-core/rnaseq/releases/tag/3.11.1)] - 2023-03-31
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### Credits
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Special thanks to the following for their code contributions to the release:
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- [Adam Talbot](https://github.com/adamrtalbot)
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- [Rob Syme](https://github.com/robsyme)
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- [suhrig](https://github.com/suhrig)
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### Enhancements & fixes
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- [[#987](https://github.com/nf-core/rnaseq/pull/987)] - Fix issue with incorrect cacheing of test datasets during CI/CD
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- [[#988](https://github.com/nf-core/rnaseq/issues/988)] - `DESEQ2_QC_STAR_SALMON` fails when sample names have many components
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- Remove `wait: false` option from Tower Actions which is the default
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- Fix release trigger for full-sized multi-cloud tests
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- Adding `[ci fast]` to commit message now skips all tests except for standard `-profile test` pipeline run
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## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-30
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### Credits

‎bin/deseq2_qc.r‎

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@@ -77,10 +77,10 @@ decompose <- n_components!=1 && all(sapply(name_components, length)==n_com
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coldata <- data.frame(samples.vec, sample=samples.vec, row.names=1)
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if (decompose) {
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groupings <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
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names(groupings) <- paste0("Group", 1:n_components)
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n_distinct <- sapply(groupings, function(grp) length(unique(grp)))
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groupings <- groupings[n_distinct!=1 & n_distinct!=length(samples.vec)]
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if (ncol(groupings)!=0) {
83+
names(groupings) <- paste0("Group", 1:ncol(groupings))
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coldata <- cbind(coldata, groupings)
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} else {
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decompose <- FALSE

‎modules.json‎

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},
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"umitools/dedup": {
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"branch": "master",
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"git_sha": "6d9c7e43404e20a97d2f6f88548456afe78282e6",
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"git_sha": "ffe2f5865f608848e440a52b73c304ea79aaf818",
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"installed_by": ["bam_dedup_stats_samtools_umitools"]
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},
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"umitools/extract": {
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"branch": "master",
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"git_sha": "6d9c7e43404e20a97d2f6f88548456afe78282e6",
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"installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
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"git_sha": "ffe2f5865f608848e440a52b73c304ea79aaf818",
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"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
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},
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"untar": {
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"branch": "master",

‎modules/nf-core/umitools/dedup/main.nf‎

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‎modules/nf-core/umitools/extract/main.nf‎

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‎nextflow.config‎

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@@ -261,7 +261,7 @@ manifest {
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description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
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mainScript = 'main.nf'
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nextflowVersion = '!>=22.10.1'
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version = '3.11.0'
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version = '3.11.1'
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doi = 'https://doi.org/10.5281/zenodo.1400710'
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}
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