workflow-management
Workflow for orchestrating reproducible omics pipelines with workflow engines and clear execution provenance.
npx skills add BioTender-max/awesome-bio-agent-skills --skill workflow-management --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.
# Workflow Management ## Version Compatibility Reference examples assume recent stable releases of the preferred tools, especially `Nextflow` and the other tools listed below. Before using code or command patterns, verify installed versions match the environment: - Python: `python -c "import <module>; print(<module>.__version__)"` - CLI: `<tool> --version` - If signatures differ, inspect the installed help or API and adapt the pattern instead of retrying unchanged. ## Overview Workflow for orchestrating reproducible omics pipelines with workflow engines and clear execution provenance. ## When To Use This Skill - use when the task is to organize or run a reproducible omics pipeline - use when Nextflow, Snakemake, CWL, or WDL style workflows are involved - use when a one-off analysis should be turned into a repeatable pipeline ## Quick Route - If the input is raw or minimally processed data, start with validation and QC before any modeling. - If the input is already processed, skip directly to the first workflow step that matches the user goal. - If the user asks for a biological conclusion, always produce at least one QC or confidence artifact alongside the final result. ## Progress
- Version Compatibility
- Overview
- When To Use This Skill
- Quick Route
- Progressive Disclosure
- Default Rules
- Expected Inputs
- Expected Outputs
- Preferred Tools
- Starter Pattern
- Workflow
- 1. Define the workflow boundary
- 2. Choose an engine
- 3. Separate config from logic
nextflow run main.nf \
What does the workflow-management skill do?
Workflow for orchestrating reproducible omics pipelines with workflow engines and clear execution provenance.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill workflow-management --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.