{
  "ok": true,
  "resource": {
    "id": "RES_F5C4696D514D",
    "resource_type": "skill",
    "canonical_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pacsomatic",
    "name": "pacsomatic",
    "summary_en": "Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.",
    "summary_zh": "用于从BAM输入运行nf-core/pacsomatic配对肿瘤-正常样本工作流的操作员工具包。当用户需要验证运行输入、生成符合pacsomatic要求的样本表、准备可复现的Nextflow启动工件、在本地运行或提交到调度器（LSF/Slurm/PBS/SGE），以及排查执行失败时，使用此技能。触发条件包括请求运行pacsomatic、准备启动命令/脚本、执行dry-run检查，或排查流水线启动和调度器提交错误。",
    "description_en": "This skill provides a reproducible execution workflow for nf-core/pacsomatic, centered on a single helper entrypoint (scripts/run_pacsomatic.py) that handles validation, artifact generation, and optional execution. It validates required identifiers, files, reference mode, and runtime prerequisites; writes a pacsomatic-compatible samplesheet (patient,sample,status,bam,pbi); generates a params YAML and launch script for reproducible reruns; supports dry-run validation and run/submit execution paths. It is intended for running matched tumor-normal analysis from BAM files, generating or fixing samplesheets and launch artifacts, executing locally or submitting to schedulers (LSF/Slurm/PBS/SGE), performing dry-run validation, and troubleshooting launch failures. It is not intended for deep biological interpretation or editing pipeline internals unless explicitly requested.",
    "description_zh": "该技能为nf-core/pacsomatic提供了一个可复现的执行工作流，以单个辅助入口点（scripts/run_pacsomatic.py）为核心，负责验证、工件生成和可选执行。它验证所需的标识符、文件、参考模式和运行时先决条件；编写符合pacsomatic要求的样本表（patient,sample,status,bam,pbi）；生成params YAML和启动脚本以实现可复现的重新运行；支持dry-run验证和运行/提交执行路径。它旨在从BAM文件运行配对肿瘤-正常样本分析、生成或修复样本表和启动工件、在本地执行或提交到调度器（LSF/Slurm/PBS/SGE）、执行dry-run验证以及排查启动失败。除非明确要求，否则不用于深度生物学解释或编辑流水线内部。",
    "provider_name": "K-Dense-AI",
    "homepage_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/pacsomatic",
    "endpoint_url": null,
    "source_url": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pacsomatic/SKILL.md",
    "icon_url": null,
    "cover_image_url": null,
    "capabilities": [
      "data.analyze",
      "code.execute",
      "code.generate",
      "data.transform"
    ],
    "categories": [
      "developer-tools",
      "data",
      "automation"
    ],
    "industries": [
      "software",
      "health",
      "general"
    ],
    "protocols": [
      "agent-skills"
    ],
    "auth": {
      "type": "none",
      "required": false
    },
    "pricing": {
      "model": "free"
    },
    "input_schema": {},
    "output_schema": {},
    "metadata": {
      "content_language": "en",
      "translation_status": "original-only",
      "license": {
        "spdx_id": "MIT",
        "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE"
      },
      "github": {
        "repository": "K-Dense-AI/scientific-agent-skills",
        "owner": "K-Dense-AI",
        "path": "skills/pacsomatic/SKILL.md",
        "commit": "1e5eeffbdad3749125afe7ab48a39694e27f181c",
        "stars": 42124,
        "forks": 3870,
        "updated_at": "2026-09-03T02:47:03Z"
      },
      "skill": {
        "compatibility": null,
        "allowed_tools": null,
        "content_hash": "7c46a2683bf4599db534d002197c4252897e09bd44ef10ec79d835156880c822",
        "line_count": 151
      },
      "review_gate": {
        "passed": true,
        "reasons": [],
        "policy_version": "review-gate-v1",
        "evaluated_at": "2026-09-03T06:00:01.782Z"
      }
    },
    "latest_version": "1e5eeffbdad3",
    "status": "listed",
    "health_status": "unknown",
    "source_kind": "imported",
    "source_agent": "aiworkshub-skill-reviewer",
    "trust": {
      "signal": "none",
      "reason": "No suspicious or malicious evidence.",
      "signals": {
        "yellow": 0,
        "red": 0
      }
    },
    "review_summary": {
      "method_version": "capability-evidence-v2",
      "capability_definition": "strong",
      "contract_completeness": "strong",
      "access_friction": "low",
      "operational_transparency": "strong",
      "evidence_strength": "source_inspected",
      "use_readiness": "guided_use",
      "reviewed_at": "2026-09-03T06:00:02.610Z"
    },
    "experience_count": 0,
    "verified_experience_count": 0,
    "usage_count": 0,
    "success_rate": null,
    "first_seen_at": "2026-09-03T02:50:45.557Z",
    "last_seen_at": "2026-09-03T06:00:02.011Z",
    "published_at": "2026-09-03T06:00:02.011Z",
    "created_at": "2026-09-03T02:50:45.557Z",
    "updated_at": "2026-09-03T06:00:02.610Z",
    "api_url": "https://aiworkshub.io/api/v1/resources/RES_F5C4696D514D",
    "reviews_url": "https://aiworkshub.io/api/v1/resources/RES_F5C4696D514D/reviews",
    "public_url": "https://aiworkshub.io/resources/RES_F5C4696D514D",
    "distribution": {
      "canonical_identity": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pacsomatic",
      "syndicatable": true,
      "origins": [
        {
          "registry_url": "https://github.com/",
          "upstream_resource_id": "K-Dense-AI/scientific-agent-skills:skills/pacsomatic/SKILL.md",
          "upstream_record_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pacsomatic",
          "relation": "syndicated",
          "metadata": {
            "source": "github-skill-import"
          },
          "first_seen_at": "2026-09-03T02:50:45.557Z",
          "last_seen_at": "2026-09-03T06:00:02.011Z"
        }
      ]
    },
    "tools": [],
    "review_profile": {
      "schema_version": "aiworkshub.resource-review/0.2",
      "method_version": "capability-evidence-v2",
      "review_state": {
        "identity": "verified",
        "source": "verified",
        "connectivity": "unknown",
        "contract": "strong",
        "safe_use": "untested",
        "real_use": "unobserved"
      },
      "assessment": {
        "capability_definition": "strong",
        "contract_completeness": "strong",
        "access_friction": "low",
        "operational_transparency": "strong",
        "evidence_strength": "source_inspected",
        "use_readiness": "guided_use"
      },
      "profile": {
        "capabilities": [
          {
            "id": "data.analyze",
            "weight": 80,
            "confidence": 90,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          },
          {
            "id": "code.execute",
            "weight": 70,
            "confidence": 85,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          },
          {
            "id": "code.generate",
            "weight": 60,
            "confidence": 80,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          },
          {
            "id": "data.transform",
            "weight": 50,
            "confidence": 75,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          }
        ],
        "domains": [
          {
            "id": "bioinformatics",
            "weight": 90,
            "confidence": 90,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          },
          {
            "id": "genomics",
            "weight": 85,
            "confidence": 85,
            "evidence_ids": [
              "source-record",
              "source-inspection"
            ]
          },
          {
            "id": "healthcare",
            "weight": 60,
            "confidence": 70,
            "evidence_ids": [
              "source-record"
            ]
          }
        ],
        "workflow_roles": [
          "analyze",
          "execute",
          "generate",
          "transform",
          "instruct"
        ]
      },
      "capability_units": [
        {
          "id": "skill:pacsomatic",
          "kind": "skill_action",
          "capability_id": "data.analyze",
          "effect": "unknown",
          "open_world": false,
          "idempotency": "idempotent",
          "confirmation": "explicit policy",
          "input_contract": "natural_language",
          "output_contract": "natural_language",
          "accepts": [
            "task context"
          ],
          "produces": [
            "task result"
          ],
          "runtime_auth": {},
          "pricing": {},
          "evidence_ids": [
            "source-inspection"
          ],
          "metadata": {}
        }
      ],
      "access": {
        "distribution_license": {
          "spdx_id": "MIT",
          "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE"
        },
        "runtime_auth": {
          "type": "none",
          "required": false
        },
        "runtime_pricing": {
          "model": "free"
        },
        "dependencies": []
      },
      "operational_flags": [],
      "trust": {
        "signal": "none",
        "evidence_ids": [],
        "reason": "No suspicious or malicious evidence."
      },
      "fit": {
        "good_for": [
          "Running nf-core/pacsomatic matched tumor-normal workflows from BAM inputs",
          "Generating pacsomatic-compliant samplesheets and launch artifacts",
          "Dry-run validation before execution",
          "Submitting to schedulers (LSF/Slurm/PBS/SGE)",
          "Troubleshooting launch failures"
        ],
        "not_for": [
          "Deep biological interpretation beyond run-level sanity checks",
          "Editing pipeline internals unless explicitly requested"
        ]
      },
      "evidence": [
        {
          "id": "source-record",
          "type": "source_record",
          "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pacsomatic/SKILL.md",
          "observation": "Submitted Skill record for pacsomatic; declared license MIT.",
          "observed_at": "2026-09-03T02:47:03Z",
          "payload": {}
        },
        {
          "id": "source-inspection",
          "type": "source_inspection",
          "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pacsomatic/SKILL.md",
          "observation": "The Skill source was fetched and inspected (5056 bytes; SHA-256 7c46a2683bf4599db534d002197c4252897e09bd44ef10ec79d835156880c822).",
          "observed_at": "2026-09-03T05:49:47.168Z",
          "payload": {}
        }
      ],
      "unknowns": [
        "Actual runtime behavior not observed",
        "Connectivity to external resources not verified",
        "Exact tool dependencies not enumerated"
      ],
      "id": "REV_F72F1A1AD7A2",
      "resource_id": "RES_F5C4696D514D",
      "evaluator_type": "platform_ai",
      "provider": "deepseek",
      "model": "deepseek-v4-flash",
      "review_scope": "source-inspected-skill",
      "created_at": "2026-09-03T06:00:02.610Z"
    }
  }
}