nextflow-io/agent-skills

migrate-nextflow-code

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…

لغة النص الأصلي: الإنجليزية

create-workflow

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…

لغة النص الأصلي: الإنجليزية

run-module

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

لغة النص الأصلي: الإنجليزية

install-nextflow

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.

لغة النص الأصلي: الإنجليزية

launch-workflow

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…

لغة النص الأصلي: الإنجليزية