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bio-workflow-management-cwl-workflows

82 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · productivity · 17 stars · scanned at commit 908229c

Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on Toil/Arvados/Calrissian. Use when deciding CWL (portability/provenance/regulated) vs Nextflow/WDL/Snakemake; declaring secondaryFiles for indexed companions (.bai/.fai/.dict/.tbi and the caret rule); putting resources/containers under requirements (must-hold) vs hints (advisory) to avoid silent OOM; …

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-workflow-management-cwl-workflows' ] || [ -L ~/.agents/skills/'bio-workflow-management-cwl-workflows' ]; then echo 'A skill folder named bio-workflow-management-cwl-workflows already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-workflow-management-cwl-workflows' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-workflow-management-cwl-workflows' ~/.agents/skills/'bio-workflow-management-cwl-workflows' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-workflow-management-cwl-workflows' ~/.claude/skills/'bio-workflow-management-cwl-workflows' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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