callingcards

Run the nf-core/callingcards pipeline for Calling Cards sequencing data.

1|Updated Jun 19, 2026

Search Tags:#bioinformatics #nf-core #nextflow #qc #samplesheet #callingcards

Ready to run

npx skills add https://github.com/danilomonge/nf-claw --skill callingcards

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: callingcards
Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/callingcards
Command: npx skills add https://github.com/danilomonge/nf-claw --skill callingcards

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill removes the guesswork from running the nf-core/callingcards workflow so you can process Calling Cards sequencing data with the correct inputs, parameters, and outputs every time.

Core Features & Use Cases

Samplesheet-driven execution: Launches the pipeline from a structured input file that ties each sample to its reads and barcode details.
Reference-aware processing: Supports mammalian and yeast runs with the right genome or annotation inputs for alignment and downstream analysis.
Reproducible QC and reporting: Produces organized results, pipeline metadata, and MultiQC summaries for review and sharing.

Quick Start

Tell the assistant to run the callingcards skill on your samplesheet, choose the organism type, and write the results to your desired output directory.

Frequently Asked Questions about callingcards

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

FAQPage Schema

How do I run the nf-core callingcards pipeline for Calling Cards sequencing data?▼

You run the nf-core callingcards pipeline by providing a structured samplesheet, specifying the organism type, and setting an output directory. The workflow handles read processing, insertion counting, and quality control reporting automatically.

Can I process both mammalian and yeast Calling Cards experiments with this workflow?▼

Yes, the callingcards pipeline supports both mammalian and yeast experiments. You must supply the appropriate genome or annotation reference inputs for alignment and downstream insertion counting analysis.

What do I need to include in the samplesheet for Calling Cards read processing?▼

The samplesheet must tie each sample to its corresponding sequencing reads and barcode details. This structured input drives the nf-core pipeline execution for accurate insertion counting and downstream QC.

Does the callingcards pipeline enforce parameter validation for reproducible Nextflow execution?▼

Yes, the callingcards pipeline uses nf-schema and Nextflow to enforce validated parameters for datatype, input, and output directory settings. This ensures reproducible execution and reliable quality control reporting.

What quality control outputs does the nf-core callingcards pipeline generate?▼

The callingcards pipeline produces organized results, pipeline metadata, and MultiQC summaries. These outputs allow you to review insertion counting results and share quality control reports across experiments.

Are there limitations when running Calling Cards pipelines without validated reference inputs?▼

Without the correct genome or annotation reference inputs, the callingcards pipeline cannot perform accurate alignment or insertion counting. Validated parameters for datatype and reference settings are required for successful execution.