nextflow-development
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data
by anthropicsFree
Description
nextflow-development is a skill from Anthropic's knowledge-work plugins, listed on skills.sh. It runs nf-core bioinformatics pipelines on sequencing data, such as RNA-seq, whole genome or exome sequencing, and ATAC-seq for chromatin accessibility. It works on local FASTQ files or public data. It is aimed at bench scientists and researchers without specialist bioinformatics training who need large-scale omics analyses such as differential expression, variant calling or accessibility analysis. The page sets out a checklist that the agent works through in order: acquire the data if it comes from GEO or SRA, pass an environment check, choose a pipeline with the user's confirmation, run a test profile that must pass, create a samplesheet, configure and run the pipeline with the genome confirmed by the user, and then verify the outputs. The listing shows Gen Agent Trust Hub and Socket as Pass, and Snyk as Warn. It suits life science researchers who have sequencing data and want a guided route to a standard analysis.…
Highlights
- nf-core pipelines for RNA-seq, WGS, WES and ATAC-seq
- Works from local FASTQs or public data
- Step-by-step checklist with checks
- Confirms pipeline and genome with the user
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nextflow-development FAQ
What does nextflow-development do?
It runs nf-core bioinformatics pipelines on sequencing data for RNA-seq, WGS, WES and ATAC-seq analyses.
How do I install it?
Run: npx skills add https://github.com/anthropics/knowledge-work-plugins --skill nextflow-development
Which pipelines does it name?
rnaseq, sarek and atacseq from nf-core, according to the listing.
Does it need bioinformatics training?
It is aimed at bench scientists without specialist training, and it works through a checklist with confirmations.
Has it been checked for security?
skills.sh lists three audits: Gen Agent Trust Hub Pass, Socket Pass and Snyk Warn. A Warn or Fail is worth reading before you install.
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