Alterlab Nf Core Sarek Agent Skill
Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.8.1 — builds the samplesheet.csv (patient, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4 MarkDuplicates and BQSR against the GATK GRCh38 resource bundle (dbSNP, Mills/1000G indels), and selects callers — explicitly correcting that sarek defaults to Strelka when --tools is unset (pass haplotypecaller for GATK best practice or deepvariant for CNN accuracy), with a non-Nextflow manual GATK4 fallback. Use when the user wants a variant-calling pipeline, FASTQ to VCF, germline or somatic SNV/indel calling, nf-core/sarek, GATK best-practices alignment-to-VCF, or BQSR/HaplotypeCaller/Mutect2/DeepVariant; annotate hits with alterlab-clinvar/alterlab-gnomad/alterlab-cosmic, parse VCFs with alterlab-pysam, store at scale with alterlab-tiledbvcf. Part of the AlterLab Academic Skills suite.
Install
one command, takes just this skill from the repositorynpx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-nf-core-sarekOther skills for the same job
different authors, same section of the catalogue
Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.
Build evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evidence, competitive landscapes, TAM/SAM/SOM reconciliation, forecast sensitivity, and auditable report scaffolds.
Advanced content and topic research skill that analyzes trends across Google Analytics, Google Trends, Substack, Medium, Reddit, LinkedIn, X, blogs, podcasts, and YouTube to generate data-driven article outlines based on user intent analysis
Shopify store command center. Orders, inventory, fulfillment, analytics, and store health. Works with any Shopify store via Admin API.
Production incidents dashboard. Reads ECS health, Sentry errors, CI failures. Offers to dispatch fix agents for active fires.
YOLO mode. Spawns 4 parallel C-suite agents (CEO, CTO, CFO, COO). Each analyzes the business from their perspective using ALL available data. Produces unfiltered Hard Truths report. After user types YOLO, autonomously runs the business for a day using /loop.
Research computing toolkit for optoelectronic information science and engineering, MATLAB/Octave, Python scientific analysis, signal processing, image processing, statistics, simulation, optimization, publication figures, sensor/time-series data, citation lookup, and common scientific libraries. Use when the user asks for MATLAB code, scientific Python, data analysis, plots, simulations, formulas, statistics, machine learning, optical/physical/materials computation, or reproducible research workflows.
> Verify statistics and claims in blog posts by fetching cited source URLs and checking if the claimed data actually appears on the page. Extracts all load-bearing claims (statistics, product or policy claims, ranking and comparative claims, named sources), validates cited URLs before fetching, and scores match confidence (exact match 1.0, paraphrase 0.7-0.9, not found 0.0). Flags uncited claims as UNVERIFIED. Use when user says "fact check", "verify statistics", "check sources", "validate claims", "factcheck", "source verification".
How to use it
Take alterlab-ieu/alterlab-nf-core-sarek from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.