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nfcore-sarek-wrapper
85 / 100 · Low risk
Fine to try.
By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c
ClawBio wrapper around nf-core/sarek 3.8.1 covering mapping through annotation for germline, tumor-only, and somatic paired analyses.
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 48 places.
Show 17 more
- skills/nfcore-sarek-wrapper/executor.py, line 147
proc = subprocess.Popen( - skills/nfcore-sarek-wrapper/executor.py, line 167
except subprocess.TimeoutExpired: - skills/nfcore-sarek-wrapper/executor.py, line 201
def _terminate_process_tree(proc: subprocess.Popen) -> None: - skills/nfcore-sarek-wrapper/executor.py, line 208
except (OSError, ProcessLookupError, subprocess.TimeoutExpired): - skills/nfcore-sarek-wrapper/executor.py, line 215
except (OSError, ProcessLookupError, subprocess.TimeoutExpired): - skills/nfcore-sarek-wrapper/executor.py, line 219
subprocess.run( - skills/nfcore-sarek-wrapper/executor.py, line 221
stdout=subprocess.DEVNULL, - skills/nfcore-sarek-wrapper/executor.py, line 222
stderr=subprocess.DEVNULL, - skills/nfcore-sarek-wrapper/executor.py, line 226
except (OSError, subprocess.SubprocessError): - skills/nfcore-sarek-wrapper/executor.py, line 231
except subprocess.TimeoutExpired: - skills/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py, line 1237
proc = subprocess.run( - skills/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py, line 1252
except subprocess.TimeoutExpired as exc: - skills/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py, line 1294
proc = subprocess.run( - skills/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py, line 1300
except (OSError, subprocess.SubprocessError): - skills/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py, line 1437
out = subprocess.run( - skills/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py, line 1440
except (FileNotFoundError, OSError, subprocess.TimeoutExpired): - skills/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py, line 1448
out = subprocess.run(
and 28 more places
Changes files outside its own folder
The author does not mention this.
Found in 3 places.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'nfcore-sarek-wrapper' ] || [ -L ~/.agents/skills/'nfcore-sarek-wrapper' ]; then echo 'A skill folder named nfcore-sarek-wrapper 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/nfcore-sarek-wrapper' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/nfcore-sarek-wrapper' ~/.agents/skills/'nfcore-sarek-wrapper' && 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/'nfcore-sarek-wrapper' ~/.claude/skills/'nfcore-sarek-wrapper' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for lilinji/GeneTind-Life-Skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/lilinji/GeneTind-Life-Skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-11 | 908229c | 85 |
Also found in
Identical copies of this skill exist at:
- stanfish06/skillquarium/skills/nfcore-sarek-wrapper