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Sequencing pipeline runner
Point it at sequencing data or a public set. Get an nf-core pipeline run for RNA-seq, variants or ATAC-seq.
Sequencing pipeline runner is a free AI skill for the job "Build and ship software". Give the instructions to an AI assistant that supports the required files and tools, then review its output.
Free · No account · Apache 2.0 licence · Made by Anthropic · Level: expert · Thinking: high
Made by Anthropic. See the original on GitHub; we copied it as it is, with its licence.
What it does
A finished nf-core pipeline run on your sequencing data, for RNA-seq, variant calling or ATAC-seq, set up for people without a bioinformatics background. It can start from FASTQ files you have or fetch a public dataset from GEO or SRA. The steps run in order, with a pause for your approval at key choices. It fetches study info and asks which samples to download. A check confirms Docker, Nextflow and Java work, with fixes if not. You confirm the pipeline, then it runs the built-in test profile, which must pass. It builds the samplesheet, confirms the genome with you, runs the full job and checks the outputs. It needs a computer with those tools.
You give it
- FASTQ files or a GEO or SRA accession
- The analysis type
- The reference genome
- A computer with Docker, Nextflow and Java
- Codebase (optional)
You get
- An environment check
- A pipeline chosen with your approval
- A samplesheet
- Completed pipeline outputs
- A verification of results
Use it when
- You have RNA-seq reads and want a differential expression analysis run for you.
- You found a public GEO dataset and want to reanalyse it.
- You need variant calling run without learning Nextflow first.
- Your pipeline failed and you suspect the environment.
How to use it
- Add it to your AI once: download it and add the folder to Claude, ChatGPT or Codex as a skill.
- Ask for the job in your own words. Your AI opens the skill when it fits.
- It works best when your AI can run code and download public data.