Nextflow Bioinformatics Development

About

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.

Key Features

• 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

Use Cases

• 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