nextflow-development Skill
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/S Published by anthropics in life-sciences.
What is nextflow-development Skill?
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/S Published by anthropics in life-sciences. This profile combines repository metadata with install, compatibility, and usage signals so developers can quickly decide whether it fits their agent workflow before opening the source repository.
Automated repository signals based on public metadata such as recency, license, installation evidence, and adoption. These are not a security audit or endorsement.
Key capabilities
- Includes SKILL.md support
- Reusable instructions support
- Testing
- Deployment
- Data analysis
- Testing use cases
- Deployment use cases
Technical details
- Install or run with Copy skill directory
When to use nextflow-development Skill
- Use it for testing.
- Use it for deployment.
- Use it for data analysis.
Built with
Editorial notes
Source
- Creator: anthropics
- Repository: anthropics/life-sciences
- Skill file: nextflow-development/SKILL.md
What it does
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/S
Skill instructions
nf-core Pipeline Deployment Run nf-core bioinformatics pipelines on local or public sequencing data. Target users: Bench scientists and researchers without specialized bioinformatics training who need to run large-scale omics analyses—differential expression, variant calling, or chromatin accessibility analysis. Workflow Checklist - [ ] Step 0: Acquire data (if from GEO/SRA) - [ ] Step 1: Environment check (MUST pass) - [ ] Step 2: Select pipeline (confirm with user) - [ ] Step 3: Run test profile (MUST pass) - [ ] Step 4: Create samplesheet - [ ] Step 5: Configure & run (confirm genome with user) - [ ] Step 6: Verify outputs --- Step 0: Acquire Data (GEO/SRA Only) Skip this step if user has local FASTQ files. For public datasets, fetch from GEO/SRA first. See references/geo-sra-acquisition.md for the full workflow. Quick start: bash 1. Get study info python scripts/srageofetch.py info GSE110004 2. Download (interactive mode) python scripts/srageofetch.py download GSE110004 -o ./fastq
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Frequently asked questions
What is nextflow-development?
nextflow-development is a open-source AI agent skill with Copy skill directory. 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.
Who is nextflow-development best for?
nextflow-development is best for reusing agent instructions, scripts, and references, testing workflows, deployment workflows, data analysis workflows.
How do I install nextflow-development?
Install or run nextflow-development using Copy skill directory. Check nextflow-development for the latest setup command.
Is nextflow-development actively maintained?
nextflow-development may need a closer maintenance check before production use.
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