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Add telomerehunter2 module - #12917

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PFRoux:add-telomerehunter2
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Add telomerehunter2 module#12917
PFRoux wants to merge 1 commit into
nf-core:masterfrom
PFRoux:add-telomerehunter2

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@PFRoux

@PFRoux PFRoux commented Sep 10, 2026

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Closes issue number #12916

This PR adds a new telomerehunter2 module.

TelomereHunter2 estimates telomere content and telomeric variant repeats from indexed BAM/CRAM sequencing data. It is a Python 3 implementation and extension of the original TelomereHunter workflow.

The module takes a coordinate-sorted BAM file, BAM index and optional chromosome banding file, then emits:

  • TelomereHunter2 summary table
  • telomeric variant repeat top-context table
  • singleton repeat table
  • full TelomereHunter2 output directory
  • output file index
  • version information

Software requirements:

# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json

channels:
  - conda-forge
  - bioconda

dependencies:
  - bioconda::telomerehunter2=1.0.11

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