Individual skill
tooluniverse-nfcore-pipelines
Run real end-to-end bioinformatics pipelines (nf-core rnaseq, sarek, atacseq) via Nextflow + Docker/Singularity, for raw FASTQ/BAM data — either local files or public GEO/SRA datasets. Use when someone asks to "run RNA-seq alignment", "quantify gene expression from FASTQs", "call germline or somatic variants from my WGS/WES data", "run an nf-core pipeline", "analyze ATAC-seq chromatin accessibility data", "reanalyze a GEO/SRA dataset (GSE/GSM/SRR accession)", "generate a samplesheet for nf-core", or "set up Nextflow to process my sequencing data". Orchestrates the full pipeline (alignment/quantification, or variant calling, or peak calling) rather than a single step. Honest: shells out to real Nextflow/Docker; checks the environment first and stops with install instructions rather than fabricating pipeline output; always runs the pipeline's small test profile before real data.
skills/tooluniverse-nfcore-pipelines/SKILL.md
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Read excerpt
# nf-core Pipeline Orchestration
Run real nf-core bioinformatics pipelines end-to-end for bench scientists who
need alignment/quantification, variant calling, or chromatin-accessibility
analysis without hand-building a pipeline.
## Honesty contract (read first)
This skill drives **real Nextflow pipelines** on **real compute**. It must
never fabricate a pipeline result.
1. **Preflight before anything.** Run `scripts/check_environment.py`. If
Docker, Nextflow (>=23.04), or Java (>=11) is missing, print the install
plan and STOP. Do not describe hypothetical alignment/variant-calling