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ipg

Install, run, debug, cite, and extend the sanjaysgk/ipg nf-core pipeline.

Updated Apr 9, 2026
Search Tags:#documentation#pipeline#nf-core#nextflow#ipg#cryptic-peptides#immunopeptidogenomics
One-click install
npx skills add https://github.com/sanjaysgk/ipg-docs --skill ipg
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ipg
Source: https://github.com/sanjaysgk/ipg-docs/tree/main
Command: npx skills add https://github.com/sanjaysgk/ipg-docs --skill ipg

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

The ipg skill helps AI agents interact with the IPG documentation site to install, run, debug, cite, and extend the sanjaysgk/ipg nf-core pipeline.

Core Features & Use Cases

  • Install Nextflow and a container engine and pull the IPG pipeline for quick starts.
  • Look up parameters, channels, and outputs across the six nf-core subworkflows to plan runs and troubleshoot issues.
  • Cite the founding Scull et al. paper and manage per-tool attributions to ensure reproducibility in proteogenomics workflows.
  • Extend the pipeline with new subworkflows or variants and document any changes within the IPG docs.

Quick Start

Start with Get started → Quickstart to run a test profile and view the cryptic FASTA output.

Frequently Asked Questions about ipg

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I install and run the nf-core IPG pipeline for cryptic peptides?▼

To run the IPG pipeline, install Nextflow and a container engine, then pull the sanjaysgk/ipg nf-core pipeline. You can validate the setup by running a test profile to view the cryptic FASTA output.

What parameters and outputs are available in the immunopeptidogenomics subworkflows?▼

The immunopeptidogenomics pipeline includes six nf-core subworkflows. You can look up specific parameters, channels, and output deliverables across these subworkflows to plan runs and troubleshoot processing issues.

How do I cite the IPG proteogenomics workflow for reproducible research?▼

Cite the foundational Scull et al. paper for the IPG workflow and manage per-tool attributions. Proper citation of the kescull tools and pipeline ensures reproducibility in proteogenomics workflows.

Can I extend the nf-core immunopeptidogenomics pipeline with new subworkflows?▼

Yes, you can extend the IPG pipeline by adding new subworkflows or variants. Any modifications should be documented within the IPG docs to maintain accurate pipeline records.

Do I need Nextflow and a container engine to run the IPG pipeline?▼

Yes, Nextflow and a container engine are required prerequisites for the IPG pipeline. They allow you to pull the pipeline and execute the nf-core subworkflows for cryptic peptide identification.

Where can I find the cryptic FASTA deliverable in the IPG pipeline outputs?▼

The cryptic FASTA output is generated after executing the IPG pipeline subworkflows. You can locate this deliverable by running the test profile provided in the quick start documentation.

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