nextflow-development

The Skill orchestrates nf-core pipeline deployment on local FASTQ files by performing environment checks and generating samplesheets. It uses YAML configuration and Nextflow to execute pipelines like rnaseq, sarek, and atacseq.

Yes, you can process GEO or SRA datasets with nf-core. The Skill supports public GEO/SRA downloads with auto-detection, generates the corresponding samplesheet, and runs the Nextflow pipeline directly on the retrieved data.

Generating a samplesheet for nf-core rnaseq or atacseq is automated by the Skill. It detects your input data format, whether local FASTQ/BAM/CRAM or GEO/SRA downloads, and creates the samplesheet needed to start pipeline execution.

Before deploying Nextflow nf-core pipelines, you need Nextflow and the necessary environment dependencies. The Skill performs automated environment checks and robust validation to ensure your setup meets the requirements for pipeline execution.

Yes, the Skill supports BAM and CRAM files as input for sarek pipelines. It auto-detects these local sequencing data formats alongside FASTQ files and integrates them into the generated samplesheet for Nextflow execution.

If your Nextflow environment is missing dependencies, the Skill's robust validation and error handling will identify the issue during its automated environment checks. This prevents pipeline execution failures by ensuring all requirements are met first.