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Add new module: telogator2 (#11033)
* Add new module: telogator2 Add nf-core module for telogator2, a tool for allele-specific telomere length estimation and TVR characterization from long-read sequencing data (ONT/PacBio). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * add telomere test data and temporarily point to fork - Add ONT telomere reads test (exercises real analysis path) - Keep PacBio no-telomere test (exercises graceful fallback) - Temporarily override modules_testdata_base_path to pinin4fjords/test-datasets#telogator2-test-data (revert before merge) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix: combine fasta and fai into single reference channel Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix: simplify process script and assert failure on no telomere reads Remove error-catching wrapper from telogator2 process script. When no telomere reads are found the tool now fails with a clear error message, which the no-telomere test asserts against. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * refactor: emit individual files instead of directory - tlens: tlens_by_allele.tsv (primary result) - plots: *.png (allele and violin plots, optional) - qc: qc directory (stats, read lengths, metadata) Also revert modules_testdata_base_path now that nf-core/test-datasets#1947 is merged. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix: exclude non-deterministic rng.txt from snapshot The qc/rng.txt file contains a random seed that differs across runs. Assert qc output exists but don't snapshot it. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix: handle non-deterministic telogator2 outputs in tests Set fixed random seed (--rng 42) via test config. Assert tlens header structure rather than md5 since TL values vary across runs due to minimap2 non-determinism. Assert plots and qc exist without snapshotting. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix: address PR review feedback - Use module_args pattern for ext.args in test config - Snapshot output file names (not md5s) for non-deterministic outputs - Remove PNGs from stub (plots are optional) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix: make plots a required output The two main plots (all_final_alleles.png, violin_atl.png) are always produced on a successful run. Remove optional flag and add them back to the stub. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * refactor: split QC directory into individual output channels Emit cmd, stats, qc_readlens, readlens, and rng as separate channels instead of a single qc directory. Touch all QC files in stub. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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‎modules/nf-core/telogator2/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- telogator2=2.2.3

‎modules/nf-core/telogator2/main.nf‎

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process TELOGATOR2 {
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tag "${meta.id}"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ab/ab4d9d463b2866006f8cbca9fbe6f978b1803e41f2a97d9f4d3c14ff6d97822f/data'
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: 'community.wave.seqera.io/library/telogator2:2.2.3--01b2748e09721f3b' }"
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input:
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tuple val(meta), path(reads), path(reads_index)
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tuple val(meta2), path(fasta), path(fai)
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output:
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tuple val(meta), path("${prefix}/tlens_by_allele.tsv") , emit: tlens
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tuple val(meta), path("${prefix}/*.png") , emit: plots
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tuple val(meta), path("${prefix}/qc/cmd.txt") , emit: cmd
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tuple val(meta), path("${prefix}/qc/stats.txt") , emit: stats
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tuple val(meta), path("${prefix}/qc/qc_readlens.png") , emit: qc_readlens
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tuple val(meta), path("${prefix}/qc/readlens.npz") , emit: readlens
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tuple val(meta), path("${prefix}/qc/rng.txt") , emit: rng
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tuple val("${task.process}"), val('telogator2'), eval("telogator2 --version | sed 's/telogator2 //'"), emit: versions_telogator2, topic: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def ref_arg = fasta ? "--ref ${fasta}" : ""
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"""
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telogator2 \\
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-i ${reads} \\
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-o ${prefix} \\
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-p ${task.cpus} \\
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${ref_arg} \\
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${args}
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"""
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stub:
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mkdir -p ${prefix}/qc
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touch ${prefix}/tlens_by_allele.tsv
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touch ${prefix}/all_final_alleles.png
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touch ${prefix}/violin_atl.png
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touch ${prefix}/qc/cmd.txt
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touch ${prefix}/qc/qc_readlens.png
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touch ${prefix}/qc/readlens.npz
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touch ${prefix}/qc/rng.txt
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touch ${prefix}/qc/stats.txt
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"""
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}

‎modules/nf-core/telogator2/meta.yml‎

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name: "telogator2"
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description: "Allele-specific telomere length estimation and TVR characterization from long reads"
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keywords:
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- bam
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- cram
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- genomics
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- telomere
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- long-read
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- pacbio
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- nanopore
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tools:
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- "telogator2":
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description: "A method for measuring allele-specific TL and characterizing telomere variant repeat (TVR) sequences from long reads"
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homepage: "https://github.com/zstephens/telogator2"
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documentation: "https://github.com/zstephens/telogator2"
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tool_dev_url: "https://github.com/zstephens/telogator2"
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doi: "10.1093/bioinformatics/btae078"
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licence:
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- "MIT"
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args_id: "$args"
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identifier: "biotools:telogator2"
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- reads:
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type: file
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description: BAM or CRAM file of long reads (PacBio or ONT)
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pattern: "*.{bam,cram}"
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ontologies:
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- edam: http://edamontology.org/format_2572
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- reads_index:
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type: file
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description: Index file for the input BAM/CRAM
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pattern: "*.{bai,crai}"
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ontologies: []
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- - meta2:
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type: map
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description: |
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Groovy Map containing reference information
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e.g. [ id:'genome' ]
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- fasta:
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type: file
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description: Optional reference genome FASTA file
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pattern: "*.{fa,fasta,fa.gz}"
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ontologies:
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- edam: http://edamontology.org/format_1929
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- fai:
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type: file
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description: Optional FASTA index file
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pattern: "*.fai"
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ontologies: []
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output:
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tlens:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/tlens_by_allele.tsv:
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type: file
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description: TSV file with telomere length estimates per allele
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pattern: "*/tlens_by_allele.tsv"
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ontologies:
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- edam: http://edamontology.org/format_3475
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plots:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/*.png:
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type: file
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description: PNG plots including allele visualizations and violin plots
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pattern: "*/*.png"
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ontologies:
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- edam: http://edamontology.org/format_3603
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cmd:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/qc/cmd.txt:
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type: file
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description: Text file recording the telogator2 command that was run
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pattern: "*/qc/cmd.txt"
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ontologies: []
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stats:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/qc/stats.txt:
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type: file
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description: Text file with QC statistics including read counts and telomere read filtering
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pattern: "*/qc/stats.txt"
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ontologies: []
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qc_readlens:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/qc/qc_readlens.png:
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type: file
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description: PNG plot of read length distribution
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pattern: "*/qc/qc_readlens.png"
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ontologies:
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- edam: http://edamontology.org/format_3603
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readlens:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/qc/readlens.npz:
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type: file
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description: Numpy compressed array of read length data
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pattern: "*/qc/readlens.npz"
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ontologies: []
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rng:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/qc/rng.txt:
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type: file
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description: Text file recording the random seed used
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pattern: "*/qc/rng.txt"
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ontologies: []
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versions_telogator2:
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- - ${task.process}:
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type: string
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description: The name of the process
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- telogator2:
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type: string
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description: The name of the tool
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- "telogator2 --version | sed 's/telogator2 //'":
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - ${task.process}:
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type: string
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description: The name of the process
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- telogator2:
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type: string
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description: The name of the tool
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- "telogator2 --version | sed 's/telogator2 //'":
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@pinin4fjords"
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maintainers:
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- "@pinin4fjords"

‎modules/nf-core/telogator2/tests/main.nf.test‎

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// nf-core modules test telogator2
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nextflow_process {
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name "Test Process TELOGATOR2"
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script "../main.nf"
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process "TELOGATOR2"
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config "./nextflow.config"
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tag "modules"
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tag "modules_nfcore"
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tag "telogator2"
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test("homo_sapiens - ont bam - telomere reads") {
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when {
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params {
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module_args = '--rng 42'
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}
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process {
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"""
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input[0] = [
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[ id:'test_tel' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_telomere/HG002_ont_tel_sub.bam', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_telomere/HG002_ont_tel_sub.bam.bai', checkIfExists: true)
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]
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input[1] = [ [ id:'genome' ], [], [] ]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert path(process.out.tlens.get(0).get(1)).readLines().first() ==
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'#chr\tposition\tref_samp\tallele_id\tTL_p75\tread_TLs\tread_lengths\tread_mapq\ttvr_len\ttvr_consensus\tsupporting_reads' },
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{ assert process.out.plots },
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{ assert snapshot(
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file(process.out.tlens.get(0).get(1)).name,
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process.out.plots.collect { meta, pngs -> pngs.collect { png -> file(png).name } },
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process.out.cmd,
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process.out.stats,
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process.out.qc_readlens,
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process.out.readlens,
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process.out.rng,
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process.out.findAll { key, val -> key.startsWith('versions') }
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).match() }
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)
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}
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}
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test("homo_sapiens - pacbio bam - no telomere reads") {
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when {
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params {
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module_args = '--rng 42'
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}
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process {
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"""
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input[0] = [
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[ id:'test' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true)
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]
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input[1] = [ [ id:'genome' ], [], [] ]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.failed },
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{ assert process.stdout.toString().contains('No telomere reads found') }
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)
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}
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}
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test("homo_sapiens - pacbio bam - stub") {
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options "-stub"
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when {
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params {
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module_args = '--rng 42'
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}
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process {
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"""
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input[0] = [
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[ id:'stub' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true)
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]
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input[1] = [ [ id:'genome' ], [], [] ]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(sanitizeOutput(process.out)).match() }
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)
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}
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}
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}

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