36 lines
1.0 KiB
Python
Executable File
36 lines
1.0 KiB
Python
Executable File
#!/usr/bin/env python3
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"""Skill wrapper for the rnaseq_sample_qc CLI stage."""
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from __future__ import annotations
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import argparse
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import subprocess
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import sys
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from pathlib import Path
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PROJECT_ROOT = Path(__file__).resolve().parents[2]
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CLI = PROJECT_ROOT / "apps" / "cli" / "run_rnaseq_sample_qc.py"
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def main() -> int:
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parser = argparse.ArgumentParser(description="RNA-seq sample QC skill wrapper")
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parser.add_argument("--workspace", required=True)
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parser.add_argument("--prefix", default="")
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parser.add_argument("--job-id", default="")
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parser.add_argument("--config", default="")
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parser.add_argument("--count-matrix", default="")
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args = parser.parse_args()
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cmd = [sys.executable, str(CLI), "--workspace", args.workspace]
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for key in ("prefix", "job_id", "config", "count_matrix"):
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value = getattr(args, key)
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if value:
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cmd.extend(["--" + key.replace("_", "-"), value])
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return subprocess.call(cmd, cwd=str(PROJECT_ROOT))
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if __name__ == "__main__":
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raise SystemExit(main())
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