modules/hlala_typing

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

hlahlalahla_typinghlala_typing

https://github.com/nf-core/modules/[...]/modules/nf-core/hlala/typing

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`results`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}`
`:directory`

Per-sample HLA-LA output directory

`extraction`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}/extraction.bam`
`:file`

Extraction BAM file

*.bam

`extraction_index`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}/extraction.bam.bai`
`:file`

Extraction BAM index file

*.bam.bai

`extraction_mapped`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}/extraction_mapped.bam`
`:file`

Extraction mapped BAM file

*.bam

`extraction_unmpapped`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}/extraction_unmapped.bam`
`:file`

Extraction unmapped BAM file

*.bam

`hla`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}/hla/*`
`:file`

HLA results

`fastq`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}/*.fastq`
`:file`

Fastq file

*.fastq

`reads_per_level`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}/reads_per_level.txt`
`:file`

Reads per level

*.txt

`remapped`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}/remapped_with_a.bam`
`:file`

Remapped BAM file

*.bam

`remapped_index`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`${prefix}/remapped_with_a.bam.bai`
`:file`

Remapped BAM index file

*.bam.bai

`versions_hlala`

`${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

Topics

name:type

description

pattern

`versions`

`${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

Tools

hlala
GPL

HLA typing from short and long reads

github.com/DiltheyLab/HLA-LA github.com/DiltheyLab/HLA-LA#running-hlala https://github.com/DiltheyLab/HLA-LA 10.1093/bioinformatics/btz235

modules/hlala_typing

Description

Input

meta:map

bam:file

bai:file

graph:directory

Output

results

meta:map

${prefix}:directory

extraction

meta:map

${prefix}/extraction.bam:file

extraction_index

meta:map

${prefix}/extraction.bam.bai:file

extraction_mapped

meta:map

${prefix}/extraction_mapped.bam:file

extraction_unmpapped

meta:map

${prefix}/extraction_unmapped.bam:file

hla

meta:map

${prefix}/hla/*:file

fastq

meta:map

${prefix}/*.fastq:file

reads_per_level

meta:map

${prefix}/reads_per_level.txt:file

remapped

meta:map

${prefix}/remapped_with_a.bam:file

remapped_index

meta:map

${prefix}/remapped_with_a.bam.bai:file

versions_hlala

${task.process}:string

hla-la:string

echo 1.0.4:eval

Topics

versions

${task.process}:string

hla-la:string

echo 1.0.4:eval

Tools

hlala GPL

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`graph`
`:directory`

`results`

`meta`
`:map`

`${prefix}`
`:directory`

`extraction`

`meta`
`:map`

`${prefix}/extraction.bam`
`:file`

`extraction_index`

`meta`
`:map`

`${prefix}/extraction.bam.bai`
`:file`

`extraction_mapped`

`meta`
`:map`

`${prefix}/extraction_mapped.bam`
`:file`

`extraction_unmpapped`

`meta`
`:map`

`${prefix}/extraction_unmapped.bam`
`:file`

`hla`

`meta`
`:map`

`${prefix}/hla/*`
`:file`

`fastq`

`meta`
`:map`

`${prefix}/*.fastq`
`:file`

`reads_per_level`

`meta`
`:map`

`${prefix}/reads_per_level.txt`
`:file`

`remapped`

`meta`
`:map`

`${prefix}/remapped_with_a.bam`
`:file`

`remapped_index`

`meta`
`:map`

`${prefix}/remapped_with_a.bam.bai`
`:file`

`versions_hlala`

`${task.process}`
`:string`

`hla-la`
`:string`

`echo 1.0.4`
`:eval`

`versions`

`${task.process}`
`:string`

`hla-la`
`:string`

`echo 1.0.4`
`:eval`

hlala
GPL