Nextflow Registry | nf-core/seq2hla@0.0.0-6c4ed3a

nf-core/seq2hla @ 0.0.0-6c4ed3a

Precision HLA typing and expression from RNA-seq data using seq2HLA

hla typing rna-seq genomics immunogenetics

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @FriederikeHanssen

Maintainers: @FriederikeHanssen

Precision HLA typing and expression from RNA-seq data using seq2HLA

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

include { SEQ2HLA } from 'nf-core/seq2hla'

MIT License

Process

`Name`	`SEQ2HLA`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`reads` file	Paired-end FASTQ files for RNA-seq data `*.{fastq.gz,fq.gz}`

Output 14 channels

#1 ambiguity tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.ambiguity` file	HLA typing ambiguity results `*.ambiguity`

#2 class1_bowtielog tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*ClassI-class.bowtielog` file	HLA Class I Bowtie alignment log `*ClassI-class.bowtielog`

#3 class2_bowtielog tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*ClassII.bowtielog` file	HLA Class II Bowtie alignment log `*ClassII.bowtielog`

#4 versions_seq2hla tuple

`${task.process}` string	The name of the process
`seq2hla` string	The name of the tool
`seq2HLA --version \| sed 's/seq2HLA.py //'` eval	The expression to obtain the version of the tool

#5 class1_expression tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*ClassI-class.expression` file	HLA Class I expression results `*ClassI-class.expression`

#6 class2_expression tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*ClassII.expression` file	HLA Class II expression results `*ClassII.expression`

#7 class1_genotype_2d tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*ClassI-class.HLAgenotype2digits` file	HLA Class I 2-digit genotype results `*ClassI-class.HLAgenotype2digits`

#8 class1_genotype_4d tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*ClassI-class.HLAgenotype4digits` file	HLA Class I 4-digit genotype results `*ClassI-class.HLAgenotype4digits`

#9 class2_genotype_2d tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*ClassII.HLAgenotype2digits` file	HLA Class II 2-digit genotype results `*ClassII.HLAgenotype2digits`

#10 class2_genotype_4d tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*ClassII.HLAgenotype4digits` file	HLA Class II 4-digit genotype results `*ClassII.HLAgenotype4digits`

#11 class1_nonclass_bowtielog tuple


`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`