Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflow-management-cwl-workflows

Maintainer FreedomIntelligence · Last updated April 1, 2026

Write Common Workflow Language (CWL) portable workflow definitions.

OpenClawNanoClawAnalysisReproductionbio-workflow-management-cwl-workflows🧠 bioos extended suitebioos extended bioinformatics suitewrite

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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.

Source Doc

Excerpt From SKILL.md

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

Use cases

Use bio-workflow-management-cwl-workflows for genomics and bioinformatics workflows.
Apply bio-workflow-management-cwl-workflows to sequencing, variant, or omics analysis tasks.