nf-core cortana-AI-powered Nextflow pipeline assistant

Example

Assisting with the setup of an RNA-seq pipeline using nf-core/rnaseq while ensuring optimal resource allocation for a cloud environment.

Scenario

A researcher starting with nf-core pipelines may need to tailor the default pipeline to a new cloud infrastructure, like setting up Azure Batch, and Cortana would guide them through custom parameter tuning and resource management to reduce costs and increase efficiency.

Example

Identifying bottlenecks in a ChIP-seq pipeline that is failing during the peak-calling stage due to improper software dependencies or batch system misconfigurations.

Scenario

An advanced bioinformatician running a ChIP-seq analysis on LSF batch processing encounters errors related to tool dependencies and resource limits. Cortana would help identify and rectify the cause, ensuring smooth execution of the pipeline.

Example

Guiding a user through writing a DSL2-compliant pipeline for a new type of sequencing analysis that isn't yet part of the nf-core catalog.

Scenario

A developer creating a custom Nextflow pipeline for single-cell RNA sequencing needs to adhere to nf-core DSL2 standards. Cortana would provide advice on structuring the pipeline, module use, and version control best practices, ensuring future scalability and integration into nf-core repositories.