new module: telomerehunter2

Is there an existing module for this?

• I have searched for the existing module

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Further Information

Hi nf-core/modules team,

I would like to contribute a new module for TelomereHunter2.

Component name:
telomerehunter2

Tool:
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.

Bioconda package:
bioconda::telomerehunter2=1.0.11

BioContainer:
quay.io/biocontainers/telomerehunter2:1.0.11--pyhdfd78af_0

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

Local checks:

• nf-test test --tag telomerehunter2 --profile docker --update-snapshot
• nf-core modules lint telomerehunter2 --plain-text

Results:

• nf-test Docker stub test passed
• lint passed with 51 tests passed, 0 warnings, 0 failures

I am opening this issue to avoid duplicate work before submitting the PR.

Thanks!

Are you going to work on this?

• If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

Software requirements (conda)

# 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

Start with the nf-test Docker stub for the telomerehunter2 tag and review the requested inputs: coordinate-sorted BAM, BAM index, and optional chromosome banding file. The work is done when the module produces the listed TelomereHunter2 outputs, the stub test passes, and nf-core modules lint telomerehunter2 --plain-text remains clean.