数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-workflow-management-cwl-workflows

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Write Common Workflow Language (CWL) portable workflow definitions.

OpenClawNanoClaw分析处理复现实验bio-workflow-management-cwl-workflows🧠 bioos extended suitebioos extended bioinformatics suitewrite

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflow-management-cwl-workflows

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

cwlVersion：v1.2 class：CommandLineTool baseCommand：fastqc。
inputs：fastq：type：File inputBinding：position：1。
outputs：html：type：File outputBinding：glob："_fastqc.html" zip：type：File outputBinding：glob："_fastqc.zip。
.amb。
.ann。

原始文档

SKILL.md 摘录

rnaseq.cwl

cwlVersion: v1.2 class: Workflow

inputs: fastq_1: File fastq_2: File salmon_index: Directory

outputs: quant_results: type: Directory outputSource: salmon/quant_dir

steps: fastp: run: fastp.cwl in: reads_1: fastq_1 reads_2: fastq_2 out: [trimmed_1, trimmed_2, json_report]

salmon: run: salmon_quant.cwl in: index: salmon_index reads_1: fastp/trimmed_1 reads_2: fastp/trimmed_2 out: [quant_dir]


## job.yaml

fastq_1:
  class: File
  path: data/sample1_R1.fq.gz
fastq_2:
  class: File
  path: data/sample1_R2.fq.gz
salmon_index:
  class: Directory
  path: ref/salmon_index
threads: 8

Run with Docker

cwltool --docker workflow.cwl job.yaml

适用场景

Use bio-workflow-management-cwl-workflows ，用于 genomics 、 bioinformatics workflows。
Apply bio-workflow-management-cwl-workflows to sequencing，variant，或 omics analysis tasks。