Nextflow Registry | nf-core/hlala/typing@0.0.0-e2d3f0d

nf-core/hlala/typing @ 0.0.0-e2d3f0d

Performs HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph.

hla hlala hla_typing hlala_typing

Latest version: 0.0.0-e2d3f0d

Total downloads: 2

Source: nf-core/modules

Authors: @mapo9

Maintainers: @mapo9

Performs HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph.

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

include { HLALA_TYPING } from 'nf-core/hlala/typing'

MIT License

Process

`Name`	`HLALA_TYPING`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`bam` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`
`bai` file	BAM index file `*.{bai}`
`graph` directory	Path to prepared graph with hla-la --action prepareGraph

Output 11 channels

#1 hla tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/hla/*` file	HLA results

#2 fastq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/*.fastq` file	Fastq file `*.fastq`

#3 results tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}` directory	Per-sample HLA-LA output directory

#4 remapped tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/remapped_with_a.bam` file	Remapped BAM file `*.bam`

#5 extraction tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/extraction.bam` file	Extraction BAM file `*.bam`

#6 remapped_index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/remapped_with_a.bam.bai` file	Remapped BAM index file `*.bam.bai`

#7 versions_hlala tuple

`${task.process}` string	The process the versions were collected from
`hla-la` string	The name of the tool
`echo 1.0.4` eval	The expression to obtain the version of the tool

#8 reads_per_level tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/reads_per_level.txt` file	Reads per level `*.txt`

#9 extraction_index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/extraction.bam.bai` file	Extraction BAM index file `*.bam.bai`

#10 extraction_mapped tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}/extraction_mapped.bam` file	Extraction mapped BAM file `*.bam`

#11 extraction_unmpapped tuple

`meta` map	Groovy Map c