nextflow-io

nextflow-io/agent-skills

Plugin Claude Code

Plugin marketplace listing 1 plugin: nextflow.

nextflow-io/agent-skills

Plugin Claude Code

Skills for building and running Nextflow pipelines with modules from the Nextflow Registry (nf-core and more).

nextflow-io/agent-skills

Command Claude Code

Evaluate the migrate-nextflow-code skill.

nextflow-io/agent-skills

MCP server Claude CodeCodexCursor +2

MCP server "seqera", hosted remotely at mcp.seqera.io, as configured in nextflow-io/agent-skills.

nextflow-io/agent-skills

Instructions file

Instructions for nextflow-io/agent-skills, covering claude.md, what this repo is, layout, the skills and how they relate and editing skills.

nextflow-io/agent-skills

Skill Claude CodeCodex

INVOKE THIS SKILL IMMEDIATELY when user asks to: write/create/build a Nextflow pipeline or workflow, create any bioinformatics pipeline (RNA-seq, DNA-seq, variant calling, ChIP-seq, etc.), or compose/chain Nextflow modules from the Nextflow Registry. This skill handles all Nextflow workflow creation tasks.

nextflow-io/agent-skills

Skill Claude CodeCodex

Install or upgrade Nextflow on the user's machine. Use when the user wants to install Nextflow, check their current Nextflow version, upgrade Nextflow, or set up the prerequisites (Java 17+) needed to run Nextflow.

nextflow-io/agent-skills

Skill Claude CodeCodex

Launch Nextflow pipeline executions on cloud and HPC clusters via Seqera Platform. Use when the user wants to run/launch/submit a pipeline on a cloud or cluster compute environment, configure a compute environment, push pipeline changes to GitHub before launching, or sign in to Seqera Platform.

nextflow-io/agent-skills

Skill Claude CodeCodex

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).

nextflow-io/agent-skills

Skill Claude CodeCodex

Run Nextflow Registry modules natively using nextflow module commands. Use when running, listing, or getting info about Nextflow modules.