Nextflow Registry | nf-core/telomerehunter@0.0.0-6c4ed3a

nf-core/telomerehunter @ 0.0.0-6c4ed3a

In silico estimation of telomere content and composition from cancer genomes

bam genomics telomere telomerehunter cancer

Latest version: 0.0.0-6c4ed3a

Total downloads: 19

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

In silico estimation of telomere content and composition from cancer genomes

Add the following snippet to your workflow script to include this module.

include { TELOMEREHUNTER } from 'nf-core/telomerehunter'

MIT License

Process

`Name`	`TELOMEREHUNTER`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`tumor_bam` file	Indexed BAM/CRAM file of the tumor sample. CRAM files are automatically converted to BAM (telomerehunter uses pysam in BAM-only mode). `*.{bam,cram}`
`tumor_bai` file	BAM/CRAM index file for the tumor sample `*.{bai,crai}`
`control_bam` file	Optional indexed BAM/CRAM file of the control sample `*.{bam,cram}`
`control_bai` file	Optional BAM/CRAM index file for the control sample `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Reference FASTA file (required when input is CRAM) `*.{fa,fasta,fna}`
`fai` file	Reference FASTA index `*.fai`
`cytoband` file	Optional cytoband file for the reference genome. When not provided ([]), telomerehunter uses its bundled hg19 cytoband. Must be supplied for hg38 data to avoid an IndexError caused by chromosomes that are longer in hg38 than hg19. `*.txt`

Output 5 channels

#1 tumor tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/tumor_TelomerCnt_${prefix}/` directory	Directory with tumor telomere analysis results

#2 control tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/control_TelomerCnt_${prefix}/` directory	Directory with control telomere analysis results

#3 summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/${prefix}_summary.tsv` file	Combined summary TSV with telomere content estimates `*_summary.tsv`

#4 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The name of the tool
`samtools --version \|& sed '1!d; s/^.*samtools //'` eval	The expression to obtain the version of the tool

#5 versions_telomerehunter tuple

`${task.process}` string	The name of the process
`telomerehunter` string	The name of the tool
`pip show telomerehunter \| sed -n 's/^Version: //p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
telomerehunter	In silico estimation of telomere content and composition from cancer genomes	https://github.com/linasieverling/TelomereHunter

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:49:41 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ftelomerehunter/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core