marsseq

Run the pinned nf-core marsseq preprocessing pipeline from a validated samplesheet.

1|Updated Jun 19, 2026

Search Tags:#bioinformatics #preprocessing #single-cell #nf-core #nextflow #rna velocity #marsseq

Ready to run

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

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill removes the guesswork from running the nf-core marsseq pipeline by turning a samplesheet and a chosen output directory into a validated, reproducible single-cell preprocessing run.

Core Features & Use Cases

Runs the MARS-seq v2 preprocessing workflow for single-cell FASTQ data.
Supports release-pinned execution, parameter validation, and runtime provenance so runs are repeatable.
Includes RNA velocity support and release-specific documentation for users who need exact pipeline behavior.
Use it when preparing MARS-seq libraries, re-running a specific release, or debugging an engine compatibility issue.

Quick Start

Ask the Skill to run the marsseq pipeline for your samplesheet with a chosen output directory and profile.

Frequently Asked Questions about marsseq

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

FAQPage Schema

How do I run MARS-seq v2 preprocessing on single-cell FASTQ files?▼

MARS-seq v2 preprocessing requires a validated samplesheet and chosen output directory to execute the pinned nf-core pipeline through Nextflow, producing reproducible single-cell FASTQ processing results.

What format does the samplesheet need to be for nf-core marsseq pipeline execution?▼

The samplesheet requires exact validated columns and schema-validated parameters to successfully execute the nf-core marsseq pipeline, ensuring provenance-preserving Nextflow runs for your single-cell data.

Can I use MARS-seq preprocessing for RNA velocity-enabled single-cell analyses?▼

Yes, MARS-seq preprocessing supports RNA velocity-enabled analyses by running the pinned nf-core pipeline with validated parameters, allowing you to process single-cell FASTQ data for velocity calculations.

How do I re-run a specific release of the MARS-seq preprocessing pipeline?▼

Release-specific reruns are supported by running the release-pinned nf-core marsseq pipeline with validated parameters and your output directory, ensuring repeatable provenance-preserving Nextflow execution.

Do I need Nextflow installed to run the MARS-seq preprocessing workflow?▼

Yes, Nextflow is required for MARS-seq preprocessing because the workflow executes the pinned nf-core marsseq pipeline through Nextflow, ensuring runtime provenance and reproducible single-cell FASTQ processing.