Nextflow Registry | nf-core/telogator2@0.0.0-6c4ed3a

nf-core/telogator2 @ 0.0.0-6c4ed3a

Allele-specific telomere length estimation and TVR characterization from long reads

bam cram genomics telomere long-read pacbio nanopore

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

Allele-specific telomere length estimation and TVR characterization from long reads

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

include { TELOGATOR2 } from 'nf-core/telogator2'

MIT License

Process

`Name`	`TELOGATOR2`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`reads` file	BAM or CRAM file of long reads (PacBio or ONT) `*.{bam,cram}`
`reads_index` file	Index file for the input BAM/CRAM `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Optional reference genome FASTA file `*.{fa,fasta,fa.gz}`
`fai` file	Optional FASTA index file `*.fai`

Output 8 channels

#1 cmd tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/qc/cmd.txt` file	Text file recording the telogator2 command that was run `*/qc/cmd.txt`

#2 rng tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/qc/rng.txt` file	Text file recording the random seed used `*/qc/rng.txt`

#3 plots tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/*.png` file	PNG plots including allele visualizations and violin plots `/.png`

#4 stats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/qc/stats.txt` file	Text file with QC statistics including read counts and telomere read filtering `*/qc/stats.txt`

#5 tlens tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/tlens_by_allele.tsv` file	TSV file with telomere length estimates per allele `*/tlens_by_allele.tsv`

#6 readlens tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/qc/readlens.npz` file	Numpy compressed array of read length data `*/qc/readlens.npz`

#7 qc_readlens tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/qc/qc_readlens.png` file	PNG plot of read length distribution `*/qc/qc_readlens.png`

#8 versions_telogator2 tuple

`${task.process}` string	The name of the process
`telogator2` string	The name of the tool
`telogator2 --version \| sed 's/telogator2 //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
telogator2	A method for measuring allele-specific TL and characterizing telomere variant repeat (TVR) sequences from long reads	https://github.com/zstephens/telogator2

Version	0.0.0-6c4ed3a