feat: Add cluster test pipeline for SLURM and LSF#2
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jayhesselberth merged 1 commit intodevelopfrom Dec 19, 2025
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Add a test pipeline under tests/pipelines/cluster/ designed to test charmer's monitoring capabilities on HPC clusters. Features: - 12 samples creating ~76 total jobs with fan-out/fan-in DAG patterns - 4 samples designed to fail at different stages with different exit codes: - fail-oom: alignment failure (exit 137) - fail-timeout: variant calling timeout (exit 124) - fail-error: processing error (exit 1) - fail-segfault: merge segfault (exit 139) - SLURM profile for Alpine cluster (amilan partition, amc-general account) - LSF profile with rna queue configuration - Configurable job delays for testing pending job display 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Summary
tests/pipelines/cluster/for testing charmer on HPC clustersTest plan
snakemake --cores 4to verify DAG structuresnakemake --profile cluster/slurmsnakemake --profile cluster/lsf🤖 Generated with Claude Code