nextflow-development

65 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a coding skill usually runs build and test commands.

By charlieviettq/awesome-agent-skill (GitHub) · coding · 27 stars · scanned at commit c567ae4

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. Expected for a coding skill.

Found in 12 places.

.claude/skills/nextflow-development/SKILL.md, line 37python scripts/sra_geo_fetch.py info GSE110004
.claude/skills/nextflow-development/SKILL.md, line 59python scripts/check_environment.py
.claude/skills/nextflow-development/SKILL.md, line 101python scripts/detect_data_type.py /path/to/data

Show 9 more

.claude/skills/nextflow-development/SKILL.md, line 116nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test_output
.claude/skills/nextflow-development/SKILL.md, line 127ls test_output/multiqc/multiqc_report.html
.claude/skills/nextflow-development/SKILL.md, line 140python scripts/generate_samplesheet.py /path/to/data <pipeline> -o samplesheet.csv
.claude/skills/nextflow-development/SKILL.md, line 154python scripts/generate_samplesheet.py --validate samplesheet.csv <pipeline>
.claude/skills/nextflow-development/SKILL.md, line 185python scripts/manage_genomes.py check <genome>
.claude/skills/nextflow-development/SKILL.md, line 205nextflow run nf-core/<pipeline> \
.claude/skills/nextflow-development/SKILL.md, line 222--max_cpus 8 --max_memory '32.GB' --max_time '24.h'
.claude/skills/nextflow-development/SKILL.md, line 232ls results/multiqc/multiqc_report.html
.claude/skills/nextflow-development/SKILL.md, line 259nextflow run nf-core/<pipeline> -resume

Downloads and installs other software

The author does not mention this.

Found in 7 places.

.claude/skills/nextflow-development/SKILL.md, line 76| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |
.claude/skills/nextflow-development/SKILL.md, line 83| Not installed / < 11 | `sudo apt install openjdk-11-jdk` |
.claude/skills/nextflow-development/references/geo-sra-acquisition.md, line 415pip install requests pyyaml

Show 4 more

.claude/skills/nextflow-development/references/installation.md, line 15curl -s https://get.nextflow.io | bash
.claude/skills/nextflow-development/references/installation.md, line 28sudo apt-get update && sudo apt-get install docker.io
.claude/skills/nextflow-development/references/installation.md, line 46sudo apt-get install singularity-container
.claude/skills/nextflow-development/references/installation.md, line 62pip install nf-core

Changes files outside its own folder

The author does not mention this.

Found in 4 places.

.claude/skills/nextflow-development/SKILL.md, line 76| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |
.claude/skills/nextflow-development/references/installation.md, line 16mv nextflow ~/bin/
.claude/skills/nextflow-development/references/installation.md, line 56echo 'export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"' >> ~/.bashrc

Show 1 more

.claude/skills/nextflow-development/references/installation.md, line 94echo 'export PATH="$HOME/bin:$PATH"' >> ~/.bashrc

Sends data to these websites: get.nextflow.io

The author does not mention this.

Found in 2 places.

.claude/skills/nextflow-development/SKILL.md, line 76| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |
.claude/skills/nextflow-development/references/installation.md, line 15curl -s https://get.nextflow.io | bash

Safer alternatives

Low-risk skills in the same category (coding) that look related. Check that one does what you need.

Other copies in this repository

charlieviettq/awesome-agent-skill has 3 more folders with a skill named nextflow-development. This page shows the lowest-scoring copy.

plugins/knowledge-work-all/skills/nextflow-development 65/100 · Review before installing
.cursor/skills/knowledge-work/bio-research/nextflow-development 65/100 · Review before installing
plugins/knowledge-work-bio-research/skills/nextflow-development 65/100 · Review before installing

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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/charlieviettq/awesome-agent-skill' "$d" && git -C "$d" checkout --quiet 'c567ae426d55fa498e919fc0f5a37c582d5c7a2c' -- '.claude/skills/nextflow-development' && mkdir -p ~/.agents/skills && cp -R "$d"/'.claude/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
2026-11-07	`c567ae4`	85