Is this skill suitable for production bioinformatics?

While it provides a robust framework based on community standards, users should always validate their environment and verify outputs as part of a standard research or clinical workflow.

How does the skill handle failed pipeline runs?

It utilizes Nextflow's native '-resume' flag, allowing you to fix configuration issues or environment errors and pick up the analysis exactly where it left off.

What software dependencies are required?

You will need Nextflow, Docker (or Singularity/Apptainer for HPC), and Java 11+. The skill includes an environment check script to help you verify and install these.

Which nf-core pipelines are supported by this skill?

The skill currently provides specialized support for nf-core/rnaseq (gene expression), nf-core/sarek (variant calling), and nf-core/atacseq (chromatin accessibility).

Can I use this to analyze public data from GEO or SRA?

Yes, the skill includes workflows to fetch metadata, download sequencing data, and generate samplesheets directly from GEO/SRA accessions using the SRA Toolkit.

Nextflow Bioinformatics Development

Name: Nextflow Bioinformatics Development
Author: anthropics

byanthropics

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147

Ciencia de Datos y ML

Automates the deployment and management of nf-core bioinformatics pipelines for large-scale genomic data analysis.

Acerca de

This skill empowers researchers and bench scientists to execute standardized nf-core bioinformatics pipelines—specifically RNA-seq, Sarek (WGS/WES), and ATAC-seq—without requiring deep command-line expertise. It manages the entire analysis lifecycle, including fetching public datasets from GEO/SRA, performing environmental health checks for Docker and Nextflow, automatically generating validated samplesheets, and executing containerized workflows with built-in resume capabilities for robust data processing.

Características Principales

Smart samplesheet generation and validation for multiple pipeline types
Automated GEO/SRA data acquisition and FASTQ downloading
Integrated support for nf-core/rnaseq, nf-core/sarek, and nf-core/atacseq
Pre-flight environment validation for Docker, Nextflow, and Java
Checkpoint-based execution with Nextflow resume functionality
147 GitHub stars

Casos de Uso

Analyzing chromatin accessibility and peak calling for ATAC-seq experiments
Quantifying gene expression from local FASTQ files or public NCBI accessions
Performing germline or somatic variant calling using the Sarek pipeline

Acerca de

Características Principales

Smart samplesheet generation and validation for multiple pipeline types
Automated GEO/SRA data acquisition and FASTQ downloading
Integrated support for nf-core/rnaseq, nf-core/sarek, and nf-core/atacseq
Pre-flight environment validation for Docker, Nextflow, and Java
Checkpoint-based execution with Nextflow resume functionality
147 GitHub stars

Casos de Uso

Analyzing chromatin accessibility and peak calling for ATAC-seq experiments
Quantifying gene expression from local FASTQ files or public NCBI accessions
Performing germline or somatic variant calling using the Sarek pipeline