Nextflow Development
Skill Verifiziert AktivRun 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.
To simplify and automate complex omics data analysis for researchers by leveraging nf-core pipelines through an AI agent.
Funktionen
- Automated GEO/SRA data acquisition
- FASTQ, BAM, CRAM file processing
- Sample sheet generation for multiple pipelines
- Environment and resource validation
- Pipeline execution orchestration via Nextflow
Anwendungsfälle
- Analyzing RNA-seq data for gene expression
- Performing variant calling on WGS/WES data
- Investigating chromatin accessibility with ATAC-seq
- Reanalyzing public datasets from GEO/SRA
Nicht-Ziele
- Performing the bioinformatics analysis itself (delegated to nf-core pipelines)
- Managing computational infrastructure (relies on Nextflow/Docker)
- Providing direct interpretation of analysis results
Workflow
- Acquire data (if from GEO/SRA)
- Check environment (Docker, Nextflow, Java)
- Detect data type and suggest pipeline
- Generate samplesheet
- Configure and run nf-core pipeline
- Verify outputs
Praktiken
- Bioinformatics workflow automation
- Data acquisition and preparation
- Pipeline execution management
Voraussetzungen
- Docker installed and running
- Nextflow version >= 23.04
- Java version >= 11
- Network access to NCBI, ENA, Docker Hub, and GitHub
Installation
Zuerst Marketplace hinzufügen
/plugin marketplace add anthropics/knowledge-work-plugins/plugin install bio-research@knowledge-work-pluginsQualitätspunktzahl
VerifiziertVertrauenssignale
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