nextflow-development

Nextflow Development is a workflow-automation skill for running nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. It solves a real friction point for bench scientists without specialized bioinformatics training: standing up and correctly configuring Nextflow pipelines for gene-expression, variant-calling, or chromatin-accessibility analysis on either local FASTQ files or public GEO/SRA datasets. It provides a stepwise checklist that enforces environment validation and test runs before touching real data.

The skill bundles SKILL.md with reference docs (installation, troubleshooting, per-pipeline guides, GEO/SRA acquisition) and Python helper scripts for environment checks, data-type detection, GEO/SRA fetching via NCBI utilities, samplesheet generation, and genome management, plus YAML pipeline/genome configs. The documented workflow runs official nf-core pipelines through Nextflow with Docker (or Singularity on HPC), verifies MultiQC reports and success markers, and confirms genome and pipeline choices with the user at explicit decision points. Installation guidance references the standard official Nextflow install (curl to bash) and Docker/Java setup, and the scripts download public sequencing data from GEO/SRA.

Target users are life-science researchers and lab scientists who need reproducible large-scale omics analysis without deep pipeline expertise, as well as bioinformatics support staff. Because it orchestrates heavyweight external tooling (Docker containers, Nextflow, large public datasets), it is more operationally involved than a pure guide, but its actions are standard, read-oriented scientific data processing driven by official, well-known pipelines.