nextflow plugins

by OpenAI

Guided NGS intake, local execution, and public-pipeline routing for BCL, FASTQ, DNA variant, RNA-seq, single-cell, epigenomics, amplicon, and metagenomics analyses, with deeper decision skills for high-risk assay branches.

by BioNexus Team

Scientific Reliability Layer & Scientific Warrant Engine for AI Agents (Warrant-First Evidence Assessment, Fail-Closed Invariants, Evidence-Capped Claims, Zero Silent Substitution).

by BioNexus Team

Scientific Reliability Layer & Scientific Warrant Engine for AI Agents (Warrant-First Evidence Assessment, Fail-Closed Invariants, Evidence-Capped Claims, Zero Silent Substitution).

by Dr. Alex M. Mawla, PhD

20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.

by Matt Corbett

Bioinformatics & genomics-pipeline team — agents (bioinformatics-workflow-architect, genomics-pipeline-engineer) for the layer answering 'which workflow engine, reference, and compute strategy, and how do we build a reproducible, validated genomics pipeline?': engine choice (Nextflow/nf-core, Snakemake, WDL+Cromwell/miniwdl, CWL), reference build (GRCh38 vs T2T-CHM13) + core steps (QC, trimming, alignment BWA-MEM2/minimap2/STAR/Salmon, dedup, variant calling GATK/DeepVariant, joint genotyping), RNA-seq (DESeq2/edgeR) and single-cell (Scanpy/Seurat), reproducibility (Docker/Apptainer, Conda/Bioconda, pinned versions, FAIR, provenance), HPC-vs-cloud scaling and cost, and validation vs GIAB/hap.py truth sets. skills, a knowledge bank (pipeline decision tree + 2026 workflow-patterns reference), and templates. Distinct from ml-engineering (generic MLOps/model training), clinical-trials (trial operations/regulatory), and data-platform (warehouse/BI). Requires ravenclaude-core@>=0.7.0.

by The Galaxy Project

Galaxy development skills: tool XML wrappers, Nextflow-to-Galaxy conversion, ToolShed revisions in usegalaxy-tools, UCSC track hubs and Galaxy Hub news posts. Mirror of galaxyproject/galaxy-skills (dev-skills/).

by OpenAI

Guided NGS intake, local execution, and public-pipeline routing for BCL, FASTQ, DNA variant, RNA-seq, single-cell, epigenomics, amplicon, and metagenomics analyses, with deeper decision skills for high-risk assay branches.