skills.rest
Revelo-RNASeq
Revelo-RNASeqOFFICIAL
Explore all skills by this author →
GitHub

rnaseq-pipeline-cleanup

Remove generated RNA-seq pipeline outputs while preserving source data and scripts.

Updated Feb 3, 2026
Search Tags:#cleanup#data management#bioinformatics#pipeline#reset#rnaseq
One-click install
npx skills add https://github.com/Revelo-RNASeq/2025_RNASeq --skill rnaseq-pipeline-cleanup
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: rnaseq-pipeline-cleanup
Source: https://github.com/Revelo-RNASeq/2025_RNASeq/tree/main/.github/skills/rnaseq-pipeline-cleanup
Command: npx skills add https://github.com/Revelo-RNASeq/2025_RNASeq --skill rnaseq-pipeline-cleanup

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides a safe and systematic way to clean up intermediate and final result files generated by an RNA-seq analysis pipeline, allowing users to reset their workspace or free up disk space without losing essential source data or scripts.

Core Features & Use Cases

  • Selective Cleanup: Offers multiple strategies to remove specific types of generated files (e.g., QC reports, analysis outputs, plots) or perform a full reset.
  • Preserves Source Data: Ensures that original FASTQ files, reference genomes, and analysis scripts remain untouched.
  • Use Case: A student has completed a demonstration of the RNA-seq pipeline and needs to reset their environment before the next session. They can use the 'full' cleanup option to remove all generated outputs, returning the project to its initial state.

Quick Start

Use the rnaseq-pipeline-cleanup skill to perform a full reset of the RNA-Seq project.

Frequently Asked Questions about rnaseq-pipeline-cleanup

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

FAQPage Schema
How do I reset my RNA-Seq analysis workspace without losing source data?▼

To reset your RNA-Seq workspace, you can perform a full cleanup that removes all generated outputs while preserving original FASTQ files, reference genomes, and analysis scripts.

Can I selectively remove RNA-Seq quantification outputs and QC reports?▼

Yes, you can selectively remove RNA-Seq quantification outputs, QC reports, analysis results, and visualizations without deleting other generated files or performing a full reset.

What is the best way to free up disk space in an RNA-seq pipeline?▼

Freeing up disk space in an RNA-seq pipeline involves systematically cleaning up intermediate and final result files, which allows efficient management without losing essential source data.

Does the RNA-seq cleanup process preserve my original FASTQ files and scripts?▼

Yes, the RNA-seq cleanup process preserves your original FASTQ files, reference genomes, and analysis scripts, ensuring that essential source data remains completely untouched during workspace resets.

How do I prepare a bioinformatics project environment for a new student session?▼

To prepare a bioinformatics project environment for a new student session, use a full cleanup option to remove all generated outputs from the RNA-seq pipeline, returning the project to its initial state.

When should I not use a full reset for my RNA-seq analysis files?▼

You should not use a full reset for your RNA-seq analysis files if you need to retain specific generated outputs like QC reports or visualizations, and should instead apply selective cleanup strategies.

Related Skills

Explore More Education & Research Skills→
ya-wayya-way

bio-workflows-rnaseq-to-de

Runs an end-to-end RNA-seq workflow from raw FASTQ files to differential expression results via picocomp.

Community
Advanced
Revelo-RNASeqRevelo-RNASeq

bio-workflows-rnaseq-to-de

Automates RNA-seq pipeline from FASTQ files to differential expression with DESeq2 and Salmon or STAR+featureCounts.

Official
Advanced
anthropicsanthropics
23.4k

nextflow-development

Automate nf-core pipeline deployment and execution for omics data analysis.

Official
Advanced
StarlitnightlyStarlitnightly
32

fastq-analysis-pipeline

Orchestrate RNA-seq analysis from FASTQ files to gene count matrices.

Community
Advanced