nextflow-development

65 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a data skill usually connects to databases or online services with your credentials.

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

Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.

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 20 places.

skills/nextflow-development/SKILL.md, line 36python scripts/sra_geo_fetch.py info GSE110004
skills/nextflow-development/SKILL.md, line 58python scripts/check_environment.py
skills/nextflow-development/SKILL.md, line 100python scripts/detect_data_type.py /path/to/data

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skills/nextflow-development/SKILL.md, line 115nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test_output
skills/nextflow-development/SKILL.md, line 126ls test_output/multiqc/multiqc_report.html
skills/nextflow-development/SKILL.md, line 139python scripts/generate_samplesheet.py /path/to/data <pipeline> -o samplesheet.csv
skills/nextflow-development/SKILL.md, line 153python scripts/generate_samplesheet.py --validate samplesheet.csv <pipeline>
skills/nextflow-development/SKILL.md, line 184python scripts/manage_genomes.py check <genome>
skills/nextflow-development/SKILL.md, line 204nextflow run nf-core/<pipeline> \
skills/nextflow-development/SKILL.md, line 221--max_cpus 8 --max_memory '32.GB' --max_time '24.h'
skills/nextflow-development/SKILL.md, line 231ls results/multiqc/multiqc_report.html
skills/nextflow-development/SKILL.md, line 258nextflow run nf-core/<pipeline> -resume
skills/nextflow-development/scripts/check_environment.py, line 58result = subprocess.run(
skills/nextflow-development/scripts/check_environment.py, line 98except subprocess.TimeoutExpired:
skills/nextflow-development/scripts/check_environment.py, line 124result = subprocess.run(
skills/nextflow-development/scripts/check_environment.py, line 165except subprocess.TimeoutExpired:
skills/nextflow-development/scripts/check_environment.py, line 191result = subprocess.run(
skills/nextflow-development/scripts/check_environment.py, line 257result = subprocess.run(
skills/nextflow-development/scripts/manage_genomes.py, line 290aws_available = subprocess.run(
skills/nextflow-development/scripts/manage_genomes.py, line 346result = subprocess.run(cmd, capture_output=True, text=True)

Downloads and installs other software

The author does not mention this.

Found in 11 places.

skills/nextflow-development/SKILL.md, line 75| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |
skills/nextflow-development/SKILL.md, line 82| Not installed / < 11 | `sudo apt install openjdk-11-jdk` |
skills/nextflow-development/references/geo-sra-acquisition.md, line 415pip install requests pyyaml

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skills/nextflow-development/references/installation.md, line 15curl -s https://get.nextflow.io | bash
skills/nextflow-development/references/installation.md, line 28sudo apt-get update && sudo apt-get install docker.io
skills/nextflow-development/references/installation.md, line 46sudo apt-get install singularity-container
skills/nextflow-development/references/installation.md, line 62pip install nf-core
skills/nextflow-development/scripts/check_environment.py, line 120fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH"
skills/nextflow-development/scripts/check_environment.py, line 187fix="Install Java 11+: sudo apt install openjdk-11-jdk"
skills/nextflow-development/scripts/check_environment.py, line 220fix="Install Java 11+: sudo apt install openjdk-11-jdk"
skills/nextflow-development/scripts/manage_genomes.py, line 297print("Install with: pip install awscli")

Changes files outside its own folder

The author does not mention this.

Found in 5 places.

skills/nextflow-development/SKILL.md, line 75| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |
skills/nextflow-development/references/installation.md, line 16mv nextflow ~/bin/
skills/nextflow-development/references/installation.md, line 56echo 'export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"' >> ~/.bashrc

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skills/nextflow-development/references/installation.md, line 94echo 'export PATH="$HOME/bin:$PATH"' >> ~/.bashrc
skills/nextflow-development/scripts/check_environment.py, line 120fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH"

Sends data to these websites: get.nextflow.io, hub.docker.com, nf-co.re

The author does not mention this. Expected for a data skill.

Found in 43 places.

skills/nextflow-development/SKILL.md, line 75| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |
skills/nextflow-development/references/installation.md, line 15curl -s https://get.nextflow.io | bash
skills/nextflow-development/scripts/check_environment.py, line 120fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH"

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skills/nextflow-development/scripts/check_environment.py, line 312import urllib.request
skills/nextflow-development/scripts/check_environment.py, line 319req = urllib.request.Request("https://hub.docker.com", headers=headers)
skills/nextflow-development/scripts/check_environment.py, line 320urllib.request.urlopen(req, timeout=10)
skills/nextflow-development/scripts/check_environment.py, line 327req = urllib.request.Request("https://nf-co.re", headers=headers)
skills/nextflow-development/scripts/check_environment.py, line 328urllib.request.urlopen(req, timeout=10)
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 15from urllib.request import Request, urlopen
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 67response = requests.get(url, timeout=10)
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 71with urlopen(req, timeout=10) as response:
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 103response = requests.get(search_url, timeout=30)
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 106with urlopen(search_url, timeout=30) as response:
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 120response = requests.get(summary_url, timeout=30)
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 123with urlopen(summary_url, timeout=30) as response:
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 160response = requests.get(search_url, timeout=30)
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 163with urlopen(search_url, timeout=30) as response:
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 176response = requests.get(summary_url, timeout=30)
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 179with urlopen(summary_url, timeout=30) as response:
skills/nextflow-development/scripts/utils/ncbi_utils.py, line 216response = requests.get(search_url, timeout=30)

and 23 more places

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Install

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

if [ -e ~/.agents/skills/'nextflow-development' ] || [ -L ~/.agents/skills/'nextflow-development' ]; then echo 'A skill folder named nextflow-development 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/nextflow-development' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/nextflow-development' ~/.agents/skills/'nextflow-development' && 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/'nextflow-development' ~/.claude/skills/'nextflow-development' (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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Score history

Date	Version	Score
2026-11-11	`908229c`	65

Also found in

Identical copies of this skill exist at:

BioTender-max/awesome-bio-agent-skills/skills/openclaw/nextflow-development