nf-core Modules for Copy Number Trajectory Analysis (coptr)

Five Nextflow modules for analyzing copy number variation trajectories from sequencing data

Overview

I have contributed five Nextflow modules to the nf-core community collection for analyzing copy number trajectories from genomic sequencing data. These modules implement the core steps of the coptr workflow:

1. coptr_index

Prepares reference genome index files for coptr analysis.

2. coptr_map

Maps sequencing reads to the reference genome and generates BAM files for downstream analysis.

3. coptr_extract

Extracts copy number information from BAM files and prepares data for trajectory analysis.

4. coptr_estimate

Estimates copy number trajectories using statistical methods to infer temporal dynamics.

5. coptr_merge

Merges and consolidates results from multiple samples for comparative analysis.