Build and debug Nextflow DSL2 pipelines and nf-core workflows.
npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill nextflow-jasrajtulsi
Please help me install this Agent Skill. Skill: nextflow Source: https://github.com/jasrajtulsi/GRAD-SCOPE/tree/main/.claude/skills/nextflow Command: npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill nextflow-jasrajtulsi
This Skill helps you build, run, configure, and debug Nextflow pipelines without having to remember every detail of the language, runtime, and deployment options.
It covers Nextflow DSL2 workflows, nf-core pipelines, modules, subworkflows, channels, processes, and configuration patterns so you can author or troubleshoot reproducible data pipelines end to end. It also supports common execution scenarios such as local runs, containerized execution, HPC schedulers, cloud executors, resource tuning, caching, resume behavior, and nf-test or lint-driven validation. Use it when you need to understand a failing run, set up profiles and containers, adapt a workflow to a new environment, or scaffold reusable scientific pipeline components.
Ask the skill to review your Nextflow project and help you run, test, or debug the workflow with clear, step-by-step guidance.
High-intent search queries and answers about installing and using this skill.
To debug a failing Nextflow pipeline run, examine process error outputs, validate channel emissions and samplesheet inputs, check resource label configurations, and inspect resume caching behavior to isolate the failing component.
Configure Nextflow DSL2 workflows for HPC by defining executor settings, resource labels, and container paths in the configuration file, ensuring modules and subworkflows match the target scheduler requirements.
Adapt an nf-core workflow by modifying configuration profiles, setting up containerized execution, validating modules with nf-test, and adjusting resource labels to match the new environment's capabilities.
Yes, Nextflow supports containerized execution, allowing you to define container images in configuration files to ensure reproducible pipeline runs across local, HPC, and cloud executors.
Nextflow resume fails when cache hashes change due to modified process scripts, altered input channels, updated samplesheets, or changed configuration parameters, requiring validation of pipeline state consistency.
The best way to validate Nextflow modules and subworkflows is using nf-test for functional testing and lint validation to enforce structure, configuration correctness, and reproducible pipeline component behavior.
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