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nfcore-scrnaseq-wrapper
90 / 100 · Low risk
Fine to try.
By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c
Wrapper skill for running nf-core/scrnaseq 4.1.0 upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA
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 45 places.
Show 17 more
- skills/nfcore-scrnaseq-wrapper/executor.py, line 144
proc = subprocess.Popen( - skills/nfcore-scrnaseq-wrapper/executor.py, line 167
except subprocess.TimeoutExpired: - skills/nfcore-scrnaseq-wrapper/executor.py, line 221
def _terminate_process_tree(proc: subprocess.Popen) -> None: - skills/nfcore-scrnaseq-wrapper/executor.py, line 230
subprocess.run( - skills/nfcore-scrnaseq-wrapper/executor.py, line 235
except (OSError, subprocess.SubprocessError): - skills/nfcore-scrnaseq-wrapper/executor.py, line 245
except (OSError, ProcessLookupError, subprocess.TimeoutExpired): - skills/nfcore-scrnaseq-wrapper/nfcore_scrnaseq_wrapper.py, line 1066
proc = subprocess.run( - skills/nfcore-scrnaseq-wrapper/nfcore_scrnaseq_wrapper.py, line 1072
except (OSError, subprocess.SubprocessError): - skills/nfcore-scrnaseq-wrapper/nfcore_scrnaseq_wrapper.py, line 1303
result = subprocess.run( - skills/nfcore-scrnaseq-wrapper/nfcore_scrnaseq_wrapper.py, line 1310
except subprocess.TimeoutExpired: - skills/nfcore-scrnaseq-wrapper/pipeline_source.py, line 33
proc = subprocess.run( - skills/nfcore-scrnaseq-wrapper/pipeline_source.py, line 42
subprocess.CalledProcessError, - skills/nfcore-scrnaseq-wrapper/pipeline_source.py, line 45
subprocess.TimeoutExpired, - skills/nfcore-scrnaseq-wrapper/preflight.py, line 60
proc = subprocess.run( - skills/nfcore-scrnaseq-wrapper/preflight.py, line 67
except (subprocess.TimeoutExpired, OSError): - skills/nfcore-scrnaseq-wrapper/preflight.py, line 274
info = subprocess.run( - skills/nfcore-scrnaseq-wrapper/preflight.py, line 281
except (subprocess.TimeoutExpired, OSError):
and 25 more places
Changes files outside its own folder
This is disclosed by the author in the skill's SKILL.md or README.
Found in 2 places.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'nfcore-scrnaseq-wrapper' ] || [ -L ~/.agents/skills/'nfcore-scrnaseq-wrapper' ]; then echo 'A skill folder named nfcore-scrnaseq-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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/nfcore-scrnaseq-wrapper' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/nfcore-scrnaseq-wrapper' ~/.agents/skills/'nfcore-scrnaseq-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-scrnaseq-wrapper' ~/.claude/skills/'nfcore-scrnaseq-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 | 90 |
Also found in
Identical copies of this skill exist at:
- stanfish06/skillquarium/skills/nfcore-scrnaseq-wrapper