Nextflow Registry | nf-core/t1k/build@0.0.0-0c7146d

nf-core/t1k/build @ 0.0.0-0c7146d

A module to create a reference database and coordinate files for T1K.

polymorphic genes HLA Kir

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @georgiakes

Maintainers: @georgiakes

A module to create a reference database and coordinate files for T1K.

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

include { T1K_BUILD } from 'nf-core/t1k/build'

MIT License

Process

`Name`	`T1K_BUILD`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`ena` file	EMBL-ENA dat file. `*.dat`
`fasta` file	FASTA file containing gene sequences. `*.fa`
`annotation` file	Gene annotation in GTF format. `*.gtf`

Output 6 channels

#1 database tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.dat` file	EMBL-ENA dat file. `*.dat`

#2 versions_t1k tuple

`${task.process}` string	The name of the process
`t1k` string	The name of the tool
`run-t1k 2>&1 \| head -n 1 \| cut -d '-' -f 1 \| cut -d v -f 2` eval	The expression to obtain the version of the tool

#3 dna_sequences tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_dna_seq.fa` file	DNA gene sequences file output. `*_dna_seq.fa`

#4 rna_sequences tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_rna_seq.fa` file	RNA gene sequences file output. `*_rna_seq.fa`

#5 dna_coordinates tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_dna_coord.fa` file	A fasta file with the coordinates of the gene alleles in the header as created form the t1k/build `*_dna_coord.fa`

#6 rna_coordinates tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_rna_coord.fa` file	A fasta file with the coordinates of the gene alleles in the header as created form the t1k/build `*_rna_coord.fa`

Tool	Description	Homepage
t1k	T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with RNA-seq, WGS or WES data.	https://github.com/mourisl/T1K/blob/v1.0.9/README.md

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:18:31 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ft1k%2Fbuild/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/t1k/build/blobs/sha256:5d3184fde2175bcfc39c38d4f71d9a16b862a61a33ee4e2e54f92219c913afb0
Size	3.0 KB
Checksum	sha256:5d3184fde2175bcfc39c38d4f71d9a16b862a61a33ee4e2e54f92219c913afb0
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:18:31 (UTC)