Alterlab Nf Core Sarek

AlterLab Creative Technologies Laboratory

Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.10.0 — 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…

Install

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-nf-core-sarek

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-nf-core-sarek -a claude-code -g

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-nf-core-sarek -a codex -g

gemini skills install https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git --path skills/bioinformatics/alterlab-nf-core-sarek

gh skill install AlterLab-IEU/AlterLab-Academic-Skills alterlab-nf-core-sarek

git clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills /tmp/AlterLab-IEU__AlterLab-Academic-Skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-nf-core-sarek ~/.claude/skills/alterlab-nf-core-sarek   # Claude Code
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-nf-core-sarek ~/.agents/skills/alterlab-nf-core-sarek   # Codex, Cursor, Gemini CLI, Copilot, OpenCode

Install

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