Individual skill

pipeline-guide

Access ENCODE uniform analysis pipelines, generate user-specific Nextflow/WDL pipelines, manage compute resources, and integrate with cloud platforms. Use when the user wants to understand ENCODE pipelines, run pipelines on their own data, generate custom Nextflow workflows from ENCODE pipeline code, check compute requirements (CPU/GPU/memory), run pipelines in background, or integrate with Google Cloud, AWS, or other cloud platforms. Also use when the user asks about ENCODE pipeline outputs, processing standards, software versions, or wants to replicate ENCODE processing. Covers local execution, HPC, and cloud deployment with resource-aware scheduling. Use this skill for ANY pipeline execution, workflow generation, or compute resource management task involving ENCODE data.

skills/pipeline-guide/SKILL.md

Source commit 36836c8725fd4d20d9c851ce314f5151aea5f57c

What was checked

Matches the observed repository HEAD

Yes

Scanner rules are current

Yes

Repository scan complete

No

Skill scan complete

No

Observed behavior

Network or broad shell

Last checked

Nov 6, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

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