#6nf-core for tailored clinical research data analysis – challenges and use cases

Clinical research data analysis poses additional requirements on data processing and management. As a core facility for clinical data analysis, we often need to maintain a balance between the demand for reproducibility and highly specific and project-tailored experimental setups and research questions.

The nf-core community offers highly standardized pipelines for the analysis of many common bioinformatics experiments, like RNA-sequencing and whole exome sequencing (WES). Our projects often require follow-up analyses after the nf-core pipeline steps. Therefore, we typically use a hybrid of Nextflow and other workflow management systems, including Snakemake, or extend pipelines with customized downstream analysis scripts.

Furthermore, due to the sensitive nature of our data a cloud-based analysis is not possible. Our computing environment needs to comply with highest security standards to protect the privacy of patients. This means we are restricted to self-contained local runs of the pipelines, once the initial setup is completed.

Here, we show a typical clinical data analysis where nf-core pipeline and tailored downstream analyses are intertwined and illustrate the privacy-ensuring computing and software installation setup.