kwp-bio-research-nextflow-development

Automate nf-core RNA-seq pipeline execution by deploying workflows that orchestrate genomic data analysis, environment validation, and public dataset acquisition to ensure reproducible computational results.

To run nf-core pipelines for variant calling, you need Docker, Nextflow, OpenJDK 11, and SRA-tools configured in your environment to ensure scalable and reproducible workflow execution.

Yes, you can automatically acquire public datasets from GEO/SRA and generate necessary samplesheets for Nextflow workflows, removing the manual data preparation barrier before running bioinformatics pipelines.

Yes, this approach supports ATAC-seq and WGS/WES workflows alongside RNA-seq analysis by orchestrating standard nf-core pipelines including rnaseq, sarek, and atacseq for comprehensive genomic data processing.

nf-core pipeline execution fails before starting when dependencies like Docker, Nextflow, and Java are incorrectly configured, which is why environment validation is performed automatically before runtime to prevent failures.