Bio Workflow Management Nextflow Pipelines
Automates and optimizes complex genomic bio workflows using Nextflow pipelines within a DevOps environment.
Install on your platform
We auto-selected Claude Code based on this skill’s supported platforms.
Run in terminal (recommended)
claude mcp add bio-workflow-management-nextflow-pipelines npx -- -y @trustedskills/bio-workflow-management-nextflow-pipelines
Or manually add to ~/.claude/settings.json
{
"mcpServers": {
"bio-workflow-management-nextflow-pipelines": {
"command": "npx",
"args": [
"-y",
"@trustedskills/bio-workflow-management-nextflow-pipelines"
]
}
}
}Requires Claude Code (claude CLI). Run claude --version to verify your install.
About This Skill
What it does
This skill enables the automation and orchestration of bioinformatics workflows using Nextflow pipelines. It allows users to define, execute, and manage complex analyses involving genomic data processing, variant calling, or other downstream tasks. The skill streamlines repetitive processes, ensures reproducibility, and facilitates collaboration among researchers.
When to use it
- Running a standard genomics analysis pipeline on a large dataset.
- Reproducing published bioinformatics results by executing the associated Nextflow workflow.
- Developing and testing new bioinformatics workflows before deployment in a production environment.
- Automating daily or weekly data processing tasks for genomic surveillance projects.
Key capabilities
- Nextflow pipeline execution
- Workflow definition using Nextflow DSL
- Parameterization of pipelines through command-line arguments
- Data input and output management within workflows
- Reproducible analysis results
Example prompts
- "Run the 'variant_calling' Nextflow pipeline with these sample files."
- "Execute the 'rnaseq_analysis' workflow, setting the number of threads to 8."
- "Show me the logs for the last execution of the 'atac_seq' pipeline."
Tips & gotchas
- Requires familiarity with Nextflow syntax and concepts.
- Ensure that all necessary dependencies (software, databases) are available in the environment where the skill is executed.
Tags
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Security Audits
| Gen Agent Trust Hub | Pass |
| Socket | Pass |
| Snyk | Pass |
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