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biomaster-workflows

biomaster-workflows，来自 FreedomIntelligence/OpenClaw-Medical-Skills 的 agent 技能。

读凭据执行命令写文件联网读文件严重 0 · 高危 6FreedomIntelligence/OpenClaw-Medical-Skills

它会碰到什么

扫了多少90 个文本文件，571 KB
它会碰到什么读凭据执行命令写文件联网读文件
命中总数77 处
命中统计严重 0 · 高 6 · 中 55 · 低 16
逐条看命中（6 条严重或高危）
  • 高 repo/agents/Biomaster.py:64cred-envread
    os.environ['USER_AGENT'] = 'Biomaster/1.0'
  • 高 repo/agents/Biomaster.py:95cred-envread
    os.environ['OPENAI_API_KEY'] = self.api_key
  • 高 repo/agents/Biomaster.py:641exec-spawn
    result = subprocess.run(["bash", shell_script_path], capture_output=True)#, text=True
  • 高 repo/agents/Knowledge.py:227cred-envread
    os.environ['OPENAI_API_KEY'] = api_key
  • 高 repo/agents/Knowledge.py:331cred-envread
    os.environ['OPENAI_API_KEY'] = api_key
  • 高 repo/scripts/run-pairsqc-merge.sh:20fs-destructive
    rm -rf $outreportdir/plots/

这一栏是扫描器报的事实，不是结论。命中多不等于有毒（安全工具、规则库、示例脚本本来就会包含危险写法），命中少也不等于干净。它和你手上的凭据、文件、网络有什么关系，需要你自己看。

技能内容

<!--

COPYRIGHT NOTICE

This file is part of the "Universal Biomedical Skills" project.

Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>

All Rights Reserved.

#

This code is proprietary and confidential.

Unauthorized copying of this file, via any medium is strictly prohibited.

#

Provenance: Authenticated by MD BABU MIA

-->

name: biomaster-workflows

description: Pipeline maestro

keywords:

  • workflows
  • RNAseq
  • ChIPseq
  • automation
  • YAML

measurable_outcome: Execute a configured pipeline end-to-end (including QC report + summary) within 24 hours of receiving inputs, logging every tool/parameter.

license: MIT

metadata:

author: BioMaster Team

version: "1.0.0"

compatibility:

  • system: Python 3.9+

allowed-tools:

  • run_shell_command
  • read_file

BioMaster Workflows

Orchestrate BioMaster’s multi-agent pipelines (RNA-seq, ChIP-seq, single-cell, Hi-C) using the provided configs and repos to deliver reproducible outputs.

Workflow

  1. Config prep: Populate YAML with tool paths, reference genomes, and workflow selection (rnaseq, chipseq, singlecell, hic).
  2. Environment: cd repo && pip install -r requirements.txt (or container) prior to running.
  3. Launch: python repo/run.py --config repo/config.yaml (or chosen config) and monitor progress.
  4. Error recovery: Let BioMaster agents retry failing stages; review logs for missing reference/index files.
  5. Output packaging: Collect BAMs/counts/peaks + QC + narrative summary of parameters and runtimes.

Guardrails

  • Fail fast when reference files or indices are absent to avoid wasted compute.
  • Record tool versions for every stage (alignment, quantification, etc.).
  • Require confirmation before deleting intermediates or rerunning destructive steps.

References

  • Full workflow descriptions, supported modalities, and repo links reside in README.md.

<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

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它属于哪个仓库

仓库FreedomIntelligence/OpenClaw-Medical-Skills
星标★ 3,010
本站分层T1
该仓技能数897
原文件路径skills/biomaster-workflows/SKILL.md

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