bio-workflow-management-cwl-workflows
Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collaborators using different systems, or contributing to community workflow registries.
npx skills add BioTender-max/awesome-bio-agent-skills --skill cwl-workflows --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: FastQC 0.12+, Nextflow 23.10+, Salmon 1.10+, Snakemake 8.0+, fastp 0.23+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # CWL Workflows **"Write a portable CWL workflow for my analysis"** → Define tools and workflows in YAML using the Common Workflow Language standard for maximum cross-platform portability and sharing through workflow registries. - CLI: `cwltool` for local execution of CWL documents - YAML: CWL v1.2 CommandLineTool and Workflow class definitions ## Basic Tool Definition ```yaml # fastqc.cwl 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" ``` ## Tool with Parameters ```yaml # bwa_mem.cwl cwlVersion: v1.2 class: CommandLineTool baseCommand: [bwa, mem] requirements: DockerRequirement:
- Version Compatibility
- Basic Tool Definition
- Tool with Parameters
- Basic Workflow
- Scatter (Parallel Execution)
- Multi-Scatter
- Input File (Job)
- Secondary Files
- Docker and Singularity
- Resource Requirements
- Conditional Steps
- Subworkflows
- File Arrays and Directories
- JavaScript Expressions
Run with Docker cwltool --docker workflow.cwl job.yaml Run with Singularity cwltool --singularity workflow.cwl job.yaml Validate CWL file cwltool --validate workflow.cwl Run workflow cwltool workflow.cwl job.yaml Run with caching cwltool --cachedir ./cache workflow.cwl job.yaml
What does the bio-workflow-management-cwl-workflows skill do?
Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collaborators using different systems, or contributing to community workflow registries.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill cwl-workflows --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.