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Found 8 Skills
Nextflow DSL 2 TDD implementation workflow. References nextflow-conventions and agent-conduct.
Migrate Nextflow pipeline code to newer language requirements. Use when fixing strict syntax errors, replacing versions channels with topic channels, migrating from `publishDir` to workflow outputs (the `output {}` block), or adding static typing (typed processes/workflows, records, typed params).
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
Use when writing or modifying Nextflow (.nf) scripts on Nextflow 25.10+ / 26.04+, especially when output may default to legacy untyped DSL2 patterns (tuple inputs, `publishDir`, `Channel.from`, `|` pipes, implicit `it`, `set`/`tap`, `splitCsv` as operator). Reference for strict syntax, typed processes, typed workflows, records, typed params, workflow output blocks, and typed operator equivalents.
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
Patterns for building, maintaining, and scaling bioinformatics workflows. Covers Nextflow, Snakemake, WDL/Cromwell, container orchestration, and best practices for reproducible computational biology. Use when ", " mentioned.
Guides users through bioinformatics analysis on AWS HealthOmics. Covers analysis type selection (alignment, variant calling, QC, interpretation), workflow generation in Nextflow or WDL, container sourcing from public registries, infrastructure setup (S3, ECR, IAM), workflow registration, parameter preparation, execution, and monitoring. Use when a user wants to run any bioinformatics pipeline on HealthOmics, set up genomics infrastructure on AWS, create a new analysis workflow, or run existing tools like BWA, GATK, DeepVariant, FastQC, or similar on HealthOmics. Triggers include "HealthOmics", "bioinformatics", "genomics pipeline", "Nextflow", "WDL", "BWA", "GATK", "DeepVariant", "FastQC", "variant calling", "alignment", "RNA-seq", "whole genome sequencing", "ECR pull-through", "workflow registration", "run cache"
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.