568 lines
20 KiB
Python
568 lines
20 KiB
Python
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#!/usr/bin/env python3
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"""Run Stage 11 Beagle imputation from one authoritative Stage10 PASS SNP VCF."""
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from __future__ import annotations
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import argparse
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from datetime import datetime, timezone
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import fcntl
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import json
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import os
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from pathlib import Path
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import re
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import shutil
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import subprocess
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import sys
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from typing import Any
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import uuid
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import zipfile
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from gfa_core.wgs_scientific_identity import build_wgs_analysis_id, sha256_file
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from gfa_core.wgs_upstream_manifest import resolve_wgs_artifacts
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STAGE = "wgs_impute"
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ROLES = (
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"imputed_snp_vcf",
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"imputed_snp_vcf_index",
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"impute_report",
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"impute_log",
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)
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def build_parser() -> argparse.ArgumentParser:
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parser = argparse.ArgumentParser(
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description="Impute the authoritative Stage10 PASS SNP VCF with Beagle"
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)
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parser.add_argument("--workspace", required=True)
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parser.add_argument("--job-id", required=True)
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parser.add_argument("--prefix", required=True)
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parser.add_argument("--filter-manifest", required=True)
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parser.add_argument("--java", default="java")
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parser.add_argument("--beagle-jar", required=True)
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parser.add_argument("--memory", default="8g")
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parser.add_argument("--window", type=float, default=40.0)
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parser.add_argument("--overlap", type=float, default=2.0)
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parser.add_argument("--ne", type=int, default=100000)
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parser.add_argument("--iterations", type=int, default=12)
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parser.add_argument("--phase-states", type=int, default=280)
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parser.add_argument("--imp-states", type=int, default=1600)
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parser.add_argument("--cluster", type=float, default=0.005)
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return parser
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def _atomic_json(path: Path, payload: dict[str, Any]) -> None:
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temporary = path.with_name(f".{path.name}.{uuid.uuid4().hex}.tmp")
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temporary.write_text(
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json.dumps(payload, ensure_ascii=False, indent=2) + "\n",
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encoding="utf-8",
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)
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os.replace(temporary, path)
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def _safe_component(value: str, label: str) -> None:
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if not re.fullmatch(r"[A-Za-z0-9][A-Za-z0-9_.-]*", value or ""):
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raise ValueError(f"{label} must be a non-empty safe path component")
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def _invocation_path(command: str) -> Path:
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resolved = shutil.which(command)
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if not resolved:
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raise RuntimeError(f"executable is unavailable: {command}")
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return Path(resolved).absolute()
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def _environment(command: str) -> dict[str, str]:
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return {
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**os.environ,
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"PATH": str(_invocation_path(command).parent)
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+ os.pathsep
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+ os.environ.get("PATH", ""),
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}
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def _java_version(java: str) -> str:
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result = subprocess.run(
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[java, "-version"],
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text=True,
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capture_output=True,
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check=False,
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env=_environment(java),
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)
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if result.returncode:
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raise RuntimeError(
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f"Java version check failed with exit code {result.returncode}"
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)
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lines = (result.stderr or result.stdout).strip().splitlines()
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if not lines:
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raise RuntimeError("Java version check produced no version")
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return lines[0]
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def _java_major(version: str) -> int:
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match = re.search(r'version\s+"([0-9]+)(?:\.([0-9]+))?', version)
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if not match:
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raise RuntimeError(f"cannot parse Java version: {version}")
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major = int(match.group(1))
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if major == 1 and match.group(2):
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major = int(match.group(2))
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return major
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def _beagle_required_java(jar: Path) -> int:
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try:
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with zipfile.ZipFile(jar) as archive:
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header = archive.read("main/Main.class")[:8]
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except (KeyError, OSError, zipfile.BadZipFile) as exc:
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raise ValueError(
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"Beagle JAR does not contain a readable main/Main.class"
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) from exc
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if len(header) < 8 or header[:4] != b"\xca\xfe\xba\xbe":
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raise ValueError("Beagle main/Main.class header is invalid")
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class_major = int.from_bytes(header[6:8], "big")
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if class_major < 45:
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raise ValueError("Beagle main/Main.class version is invalid")
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return class_major - 44
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def _validate_java_for_beagle(java_version: str, jar: Path) -> None:
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configured = _java_major(java_version)
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required = _beagle_required_java(jar)
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if configured < required:
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raise RuntimeError(
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f"Beagle requires Java {required} or newer; "
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f"configured Java is {configured}"
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)
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def _authority_header(
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path: str | Path,
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*,
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workspace: Path,
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prefix: str,
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job_id: str,
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) -> dict[str, Any]:
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try:
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manifest = json.loads(Path(path).read_text(encoding="utf-8"))
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except (OSError, UnicodeError, json.JSONDecodeError) as exc:
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raise ValueError(
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"wgs_variant_filter authority Manifest is unreadable"
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) from exc
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method = str(manifest.get("method") or "")
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if (
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not isinstance(manifest, dict)
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or manifest.get("stage") != "wgs_variant_filter"
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or manifest.get("status") != "success"
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or method not in {"gatk", "bcftools"}
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):
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raise ValueError(
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"wgs_variant_filter authority Manifest is not a legal success"
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)
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if (
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manifest.get("prefix") != prefix
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or manifest.get("job_id") != job_id
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or manifest.get("workspace") != str(workspace)
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or (manifest.get("parameters") or {}).get("method") != method
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):
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raise ValueError(
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"wgs_variant_filter authority Manifest identity mismatch"
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)
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return manifest
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def _vcf_identity(
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path: Path,
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) -> tuple[list[str], list[tuple[str, int, str, str]]]:
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import pysam
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if not path.is_file() or path.stat().st_size <= 0:
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raise RuntimeError("VCF is missing or empty")
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try:
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with pysam.VariantFile(str(path)) as vcf:
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samples = list(vcf.header.samples)
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if not samples or len(samples) != len(set(samples)):
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raise RuntimeError("VCF sample header is invalid")
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records = list(vcf)
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keys = [
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(str(record.contig), int(record.pos), record.ref, ",".join(record.alts or ()))
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for record in records
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]
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if not keys:
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raise RuntimeError("VCF has no variant records")
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contig = keys[0][0]
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with pysam.VariantFile(str(path)) as indexed:
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next(indexed.fetch(contig, 0, None), None)
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except RuntimeError:
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raise
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except Exception as exc:
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raise RuntimeError(f"VCF is invalid or its TBI is not queryable: {exc}") from exc
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return samples, keys
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def _tabix_index(path: Path) -> str:
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import pysam
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pysam.tabix_index(str(path), preset="vcf", force=True)
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return str(pysam.__version__)
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def _run_beagle(
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java: str,
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jar: Path,
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source: Path,
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output_prefix: Path,
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parameters: dict[str, Any],
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log: Any,
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) -> None:
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command = [
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java,
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f"-Xmx{parameters['memory']}",
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"-jar",
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str(jar),
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f"gt={source}",
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f"out={output_prefix}",
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f"window={parameters['window']}",
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f"overlap={parameters['overlap']}",
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f"ne={parameters['ne']}",
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f"iterations={parameters['iterations']}",
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f"phase-states={parameters['phase_states']}",
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f"imp-states={parameters['imp_states']}",
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f"cluster={parameters['cluster']}",
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]
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log.write(f"Beagle argv: {json.dumps(command)}\n")
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log.flush()
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result = subprocess.run(
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command,
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stdout=log,
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stderr=subprocess.STDOUT,
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text=True,
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check=False,
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env=_environment(java),
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)
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log.write(f"Beagle exit={result.returncode}\n")
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log.flush()
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if result.returncode:
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raise RuntimeError(
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f"Beagle failed with exit code {result.returncode}"
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)
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def _beagle_reported_version(path: Path) -> str:
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if not path.is_file() or path.stat().st_size <= 0:
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raise RuntimeError("Beagle generated log is missing or empty")
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for line in path.read_text(encoding="utf-8", errors="replace").splitlines():
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if line.strip():
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return line.strip()
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raise RuntimeError("Beagle generated log has no version evidence")
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def _artifact(
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workspace: Path, source: Path, destination: Path, role: str
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) -> dict[str, Any]:
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size = source.stat().st_size
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return {
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"artifact": role,
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"role": role,
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"path": str(destination.relative_to(workspace)),
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"full_path": str(destination.resolve()),
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"type": source.suffix.lstrip(".") or "file",
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"size": size,
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"size_bytes": size,
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"sha256": sha256_file(source),
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}
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def _publish(
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bundle: Path,
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destination: Path,
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manifest_work: Path,
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authority: Path,
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started_at: str,
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) -> bool:
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lock_path = authority.parent.parent / ".locks" / f"{authority.stem}.lock"
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lock_path.parent.mkdir(parents=True, exist_ok=True)
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with lock_path.open("a+", encoding="utf-8") as lock:
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fcntl.flock(lock.fileno(), fcntl.LOCK_EX)
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if authority.is_file():
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try:
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current = json.loads(authority.read_text(encoding="utf-8"))
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if (
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current.get("status") == "success"
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and str(current.get("start_time") or "") >= started_at
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):
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return False
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except Exception:
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pass
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destination.parent.mkdir(parents=True, exist_ok=True)
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os.replace(bundle, destination)
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os.replace(manifest_work, authority)
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return True
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def _failure(
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args: argparse.Namespace, run_id: str, started_at: str, error: str
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) -> dict[str, Any]:
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return {
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"manifest_version": "1.0",
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"stage": STAGE,
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"status": "failed",
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"prefix": args.prefix,
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"job_id": args.job_id,
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"run_id": run_id,
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"start_time": started_at,
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"artifacts": {},
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"errors": [error],
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}
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def _publish_failure(
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authority: Path,
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args: argparse.Namespace,
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run_id: str,
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started_at: str,
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error: str,
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) -> None:
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lock_path = authority.parent.parent / ".locks" / f"{authority.stem}.lock"
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lock_path.parent.mkdir(parents=True, exist_ok=True)
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with lock_path.open("a+", encoding="utf-8") as lock:
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fcntl.flock(lock.fileno(), fcntl.LOCK_EX)
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failure_path = (
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authority
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if not authority.exists()
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else authority.parent
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/ f"{args.prefix}.{STAGE}.failed.{run_id}.manifest.json"
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)
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_atomic_json(
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failure_path, _failure(args, run_id, started_at, error)
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)
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def _validated_parameters(args: argparse.Namespace) -> dict[str, Any]:
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if not re.fullmatch(r"[1-9][0-9]*[gGmMkK]", args.memory or ""):
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raise ValueError("memory must be a positive JVM size such as 8g")
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values = {
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"window": args.window,
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"overlap": args.overlap,
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"ne": args.ne,
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"iterations": args.iterations,
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"phase_states": args.phase_states,
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"imp_states": args.imp_states,
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"cluster": args.cluster,
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}
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if any(value <= 0 for value in values.values()):
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raise ValueError("all Beagle scientific parameters must be positive")
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if args.overlap >= args.window:
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raise ValueError("overlap must be smaller than window")
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return {
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"method": "beagle",
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"java": args.java,
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"beagle_jar": str(Path(args.beagle_jar).absolute()),
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"memory": args.memory.lower(),
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**values,
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}
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def run(args: argparse.Namespace) -> int:
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workspace = Path(args.workspace).resolve()
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run_id = uuid.uuid4().hex
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started_at = datetime.now(timezone.utc).isoformat()
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final = workspace / "final"
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final.mkdir(parents=True, exist_ok=True)
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try:
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_safe_component(args.prefix, "prefix")
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except ValueError as exc:
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|
|
_atomic_json(
|
||
|
|
final / f"{STAGE}.failed.{run_id}.manifest.json",
|
||
|
|
_failure(args, run_id, started_at, str(exc)),
|
||
|
|
)
|
||
|
|
print(f"{STAGE} failed: {exc}", file=sys.stderr)
|
||
|
|
return 1
|
||
|
|
authority = final / f"{args.prefix}.{STAGE}.manifest.json"
|
||
|
|
try:
|
||
|
|
parameters = _validated_parameters(args)
|
||
|
|
jar = Path(parameters["beagle_jar"])
|
||
|
|
if not jar.is_file() or jar.stat().st_size <= 0:
|
||
|
|
raise ValueError("Beagle JAR is missing or empty")
|
||
|
|
if jar.suffix.lower() != ".jar":
|
||
|
|
raise ValueError("Beagle JAR path must end in .jar")
|
||
|
|
header = _authority_header(
|
||
|
|
args.filter_manifest,
|
||
|
|
workspace=workspace,
|
||
|
|
prefix=args.prefix,
|
||
|
|
job_id=args.job_id,
|
||
|
|
)
|
||
|
|
sample_set_id = str(header.get("wgs_sample_set_id") or "")
|
||
|
|
reference_id = str(header.get("wgs_reference_id") or "")
|
||
|
|
upstream_analysis_id = str(header.get("wgs_analysis_id") or "")
|
||
|
|
upstream_method = str(header.get("method") or "")
|
||
|
|
if not sample_set_id or not reference_id or not upstream_analysis_id:
|
||
|
|
raise ValueError(
|
||
|
|
"wgs_variant_filter scientific lineage is incomplete"
|
||
|
|
)
|
||
|
|
resolved = resolve_wgs_artifacts(
|
||
|
|
args.filter_manifest,
|
||
|
|
"wgs_variant_filter",
|
||
|
|
("pass_snp_vcf", "pass_snp_vcf_index"),
|
||
|
|
expected_sample_set_id=sample_set_id,
|
||
|
|
expected_reference_id=reference_id,
|
||
|
|
expected_analysis_id=upstream_analysis_id,
|
||
|
|
expected_method=upstream_method,
|
||
|
|
)
|
||
|
|
if any(len(resolved[role]) != 1 for role in resolved):
|
||
|
|
raise RuntimeError("authoritative PASS SNP VCF and TBI must be singletons")
|
||
|
|
source = resolved["pass_snp_vcf"][0].path
|
||
|
|
source_index = resolved["pass_snp_vcf_index"][0].path
|
||
|
|
if source_index != Path(f"{source}.tbi"):
|
||
|
|
raise RuntimeError("PASS SNP VCF index is not its declared sidecar")
|
||
|
|
expected_samples = (header.get("metrics") or {}).get(
|
||
|
|
"output_sample_ids"
|
||
|
|
)
|
||
|
|
if (
|
||
|
|
not isinstance(expected_samples, list)
|
||
|
|
or not expected_samples
|
||
|
|
or len(expected_samples) != len(set(expected_samples))
|
||
|
|
or (header.get("metrics") or {}).get("input_sample_ids")
|
||
|
|
!= expected_samples
|
||
|
|
):
|
||
|
|
raise RuntimeError("wgs_variant_filter sample set is incomplete")
|
||
|
|
input_samples, input_keys = _vcf_identity(source)
|
||
|
|
if input_samples != expected_samples:
|
||
|
|
raise RuntimeError("PASS SNP VCF sample header mismatch")
|
||
|
|
java_version = _java_version(args.java)
|
||
|
|
_validate_java_for_beagle(java_version, jar)
|
||
|
|
jar_sha256 = sha256_file(jar)
|
||
|
|
attempt = workspace / ".attempts" / run_id
|
||
|
|
bundle = attempt / "bundle"
|
||
|
|
bundle.mkdir(parents=True, exist_ok=False)
|
||
|
|
beagle_prefix = attempt / "beagle"
|
||
|
|
base = f"{args.prefix}.{STAGE}.cohort"
|
||
|
|
output = bundle / f"{base}.imputed.snp.vcf.gz"
|
||
|
|
output_index = Path(f"{output}.tbi")
|
||
|
|
report = bundle / f"{args.prefix}.{STAGE}.cohort.report.md"
|
||
|
|
log_path = bundle / f"{args.prefix}.{STAGE}.cohort.impute.log"
|
||
|
|
with log_path.open("w", encoding="utf-8") as log:
|
||
|
|
_run_beagle(
|
||
|
|
args.java, jar, source, beagle_prefix, parameters, log
|
||
|
|
)
|
||
|
|
generated = Path(f"{beagle_prefix}.vcf.gz")
|
||
|
|
generated_log = Path(f"{beagle_prefix}.log")
|
||
|
|
if not generated.is_file() or generated.stat().st_size <= 0:
|
||
|
|
raise RuntimeError("Beagle output VCF is missing or empty")
|
||
|
|
shutil.move(str(generated), output)
|
||
|
|
stale_index = Path(f"{generated}.tbi")
|
||
|
|
stale_index.unlink(missing_ok=True)
|
||
|
|
pysam_version = _tabix_index(output)
|
||
|
|
beagle_version = _beagle_reported_version(generated_log)
|
||
|
|
log.write(f"Beagle reported version: {beagle_version}\n")
|
||
|
|
log.flush()
|
||
|
|
if not output_index.is_file() or output_index.stat().st_size <= 0:
|
||
|
|
raise RuntimeError("imputed SNP VCF index is missing or empty")
|
||
|
|
output_samples, output_keys = _vcf_identity(output)
|
||
|
|
if output_samples != input_samples:
|
||
|
|
raise RuntimeError("imputed SNP VCF sample header mismatch")
|
||
|
|
if output_keys != input_keys:
|
||
|
|
raise RuntimeError(
|
||
|
|
"imputed SNP VCF site keys are not conserved in input order"
|
||
|
|
)
|
||
|
|
report.write_text(
|
||
|
|
"# WGS Beagle imputation\n\n"
|
||
|
|
"- site policy: ordered (CHROM,POS,REF,ALT) keys are exactly "
|
||
|
|
"conserved; Beagle may change genotype, phase, and imputation "
|
||
|
|
"fields only.\n"
|
||
|
|
f"- samples: {len(output_samples)}\n"
|
||
|
|
f"- sites: {len(output_keys)}\n"
|
||
|
|
f"- parameters: {json.dumps(parameters, sort_keys=True)}\n",
|
||
|
|
encoding="utf-8",
|
||
|
|
)
|
||
|
|
software = {
|
||
|
|
"java": {
|
||
|
|
"path": str(_invocation_path(args.java).resolve()),
|
||
|
|
"version": java_version,
|
||
|
|
},
|
||
|
|
"beagle": {
|
||
|
|
"path": str(jar.resolve()),
|
||
|
|
"version": beagle_version,
|
||
|
|
"sha256": jar_sha256,
|
||
|
|
},
|
||
|
|
"pysam": {
|
||
|
|
"version": pysam_version,
|
||
|
|
},
|
||
|
|
}
|
||
|
|
analysis_id = build_wgs_analysis_id(
|
||
|
|
STAGE,
|
||
|
|
[item.sha256 for values in resolved.values() for item in values],
|
||
|
|
parameters,
|
||
|
|
{
|
||
|
|
"java": java_version,
|
||
|
|
"beagle": beagle_version,
|
||
|
|
"beagle_jar_sha256": jar_sha256,
|
||
|
|
},
|
||
|
|
method="beagle",
|
||
|
|
)
|
||
|
|
destination = (
|
||
|
|
final / ".wgs_impute_runs" / args.prefix / run_id
|
||
|
|
)
|
||
|
|
sources = {
|
||
|
|
"imputed_snp_vcf": output,
|
||
|
|
"imputed_snp_vcf_index": output_index,
|
||
|
|
"impute_report": report,
|
||
|
|
"impute_log": log_path,
|
||
|
|
}
|
||
|
|
artifacts = {
|
||
|
|
role: _artifact(
|
||
|
|
workspace, source_path, destination / source_path.name, role
|
||
|
|
)
|
||
|
|
for role, source_path in sources.items()
|
||
|
|
}
|
||
|
|
manifest = {
|
||
|
|
"manifest_version": "1.0",
|
||
|
|
"stage": STAGE,
|
||
|
|
"status": "success",
|
||
|
|
"prefix": args.prefix,
|
||
|
|
"job_id": args.job_id,
|
||
|
|
"run_id": run_id,
|
||
|
|
"start_time": started_at,
|
||
|
|
"workspace": str(workspace),
|
||
|
|
"method": "beagle",
|
||
|
|
"upstream_method": upstream_method,
|
||
|
|
"wgs_sample_set_id": sample_set_id,
|
||
|
|
"wgs_reference_id": reference_id,
|
||
|
|
"upstream_wgs_analysis_ids": {
|
||
|
|
"wgs_variant_filter": upstream_analysis_id
|
||
|
|
},
|
||
|
|
"wgs_analysis_id": analysis_id,
|
||
|
|
"parameters": parameters,
|
||
|
|
"software": software,
|
||
|
|
"metrics": {
|
||
|
|
"input_sample_ids": input_samples,
|
||
|
|
"output_sample_ids": output_samples,
|
||
|
|
"total_samples": len(output_samples),
|
||
|
|
"input_sites": len(input_keys),
|
||
|
|
"output_sites": len(output_keys),
|
||
|
|
"input_site_keys": [list(key) for key in input_keys],
|
||
|
|
"output_site_keys": [list(key) for key in output_keys],
|
||
|
|
},
|
||
|
|
"artifacts": artifacts,
|
||
|
|
}
|
||
|
|
manifest_work = attempt / "manifest.json"
|
||
|
|
_atomic_json(manifest_work, manifest)
|
||
|
|
if not _publish(
|
||
|
|
bundle, destination, manifest_work, authority, started_at
|
||
|
|
):
|
||
|
|
raise RuntimeError(
|
||
|
|
"stale imputation attempt cannot replace newer run"
|
||
|
|
)
|
||
|
|
return 0
|
||
|
|
except Exception as exc:
|
||
|
|
_publish_failure(authority, args, run_id, started_at, str(exc))
|
||
|
|
print(f"{STAGE} failed: {exc}", file=sys.stderr)
|
||
|
|
return 1
|
||
|
|
|
||
|
|
|
||
|
|
def main(argv: list[str] | None = None) -> int:
|
||
|
|
return run(build_parser().parse_args(argv))
|
||
|
|
|
||
|
|
|
||
|
|
if __name__ == "__main__":
|
||
|
|
raise SystemExit(main())
|