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andrewprzhclaude
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Add barcode calling CI tests for full 10x whitelists (v2 737K, v3 3M)
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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name: Barcode Mouse 10x Full Whitelist
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on:
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workflow_dispatch:
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schedule:
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- cron: '0 2 * * 6'
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env:
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LAUNCHER: ${{github.workspace}}/tests/github/run_barcode_test.py
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CFG_DIR: /abga/work/andreyp/ci_isoquant/data/barcodes
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BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/
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OUTPUT_BASE: /abga/work/andreyp/ci_isoquant/output/${{github.ref_name}}/barcodes/
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concurrency:
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group: ${{github.workflow}}
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cancel-in-progress: false
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jobs:
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check-changes:
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runs-on:
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labels: [isoquant]
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name: 'Check for recent changes'
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outputs:
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has_changes: ${{steps.check.outputs.has_changes}}
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steps:
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- name: 'Checkout'
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: 'Check for commits in last 7 days'
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id: check
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run: |
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# Always run on manual trigger
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if [ "${{github.event_name}}" = "workflow_dispatch" ]; then
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echo "has_changes=true" >> $GITHUB_OUTPUT
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exit 0
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fi
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# Check for commits in last 7 days
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COMMITS=$(git log --oneline --since="7 days ago" | wc -l)
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if [ "$COMMITS" -gt 0 ]; then
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echo "Found $COMMITS commits in last 7 days"
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echo "has_changes=true" >> $GITHUB_OUTPUT
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else
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echo "No commits in last 7 days, skipping"
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echo "has_changes=false" >> $GITHUB_OUTPUT
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fi
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launch-runner:
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needs: check-changes
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if: needs.check-changes.outputs.has_changes == 'true'
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runs-on:
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labels: [isoquant]
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name: 'Running barcode detection QC'
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steps:
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- name: 'Cleanup'
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run: >
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set -e &&
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shopt -s dotglob &&
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rm -rf *
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- name: 'Checkout'
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uses: actions/checkout@v3
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with:
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fetch-depth: 1
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- name: 'Mouse 10x v3 3M full whitelist'
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shell: bash
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env:
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STEP_NAME: Mouse.10x.v3.3M.full
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run: |
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export PATH=$PATH:${{env.BIN_PATH}}
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python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
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- name: 'Mouse 10x v2 737K full whitelist'
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shell: bash
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env:
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STEP_NAME: Mouse.10x.v2.737K.full
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run: |
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export PATH=$PATH:${{env.BIN_PATH}}
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python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

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