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Prepare to check outputs
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dfornika committed Feb 15, 2024
1 parent 4bc2804 commit 29b6257
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Showing 5 changed files with 23 additions and 2 deletions.
11 changes: 11 additions & 0 deletions .github/scripts/check_outputs.py
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#!/usr/bin/env python3

import argparse

def main(args):
pass

if __name__ == '__main__':
parser = argparse.ArgumentParser()
args = parser.parse_args()
main(args)
3 changes: 3 additions & 0 deletions .github/scripts/check_outputs.sh
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#!/bin/bash

.github/scripts/check_outputs.py
3 changes: 3 additions & 0 deletions .github/scripts/download_run_simulator.sh
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#!/bin/bash

wget https://github.com/dfornika/illumina-run-simulator/releases/download/v0.1.0/illumina-run-simulator-0.1.0-standalone.jar -O illumina-run-simulator.jar
2 changes: 2 additions & 0 deletions .github/scripts/simulate_runs.sh
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#!/bin/bash

mkdir -p artifacts/simulated_runs/{M00123,M00456,VH00123}/22

timeout 10 java -jar illumina-run-simulator.jar \
--config .github/data/illumina-run-simulator/config.edn \
2> >(tee artifacts/illumina-run-simulator.log.jsonl) \
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6 changes: 4 additions & 2 deletions .github/workflows/tests.yml
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Expand Up @@ -28,10 +28,9 @@ jobs:
java-version: '21'
- name: Download Run Simulator
run: |
wget https://github.com/dfornika/illumina-run-simulator/releases/download/v0.1.0/illumina-run-simulator-0.1.0-standalone.jar -O illumina-run-simulator.jar
bash .github/scripts/download_run_simulator.sh
- name: Simulate Runs
run: |
mkdir -p artifacts/simulated_runs/{M00123,M00456,VH00123}/22
bash .github/scripts/simulate_runs.sh
- name: Setup Python
uses: actions/setup-python@v4
Expand All @@ -40,3 +39,6 @@ jobs:
- name: Run symlink-seqs
run: |
bash .github/scripts/run_symlink-seqs.sh
- name: Check Outputs
run: |
bash .github/scripts/check_outputs.sh

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