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’, single_end:false ]

`bam:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`bai:file`

BAM index file

*.{bai}

`graph:directory`

Path to prepared graph with hla-la —acton prepareGraph

Output

name:type

description

pattern

`results`

`meta:map`

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

`${meta.id}:file`

results file

`extraction`

`meta:map`

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

`${meta.id}/extraction.bam*:file`

Extraction BAM file

*.bam*

`extraction_mapped`

`meta:map`

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

`${meta.id}/extraction_mapped.bam:file`

Extraction mapped BAM file

*.bam

`extraction_unmpapped`

`meta:map`

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

`${meta.id}/extraction_unmapped.bam:file`

Extraction unmapped BAM file

*.bam

`hla`

`meta:map`

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

`${meta.id}/hla/*:file`

HLA results

`fastq`

`meta:map`

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

`${meta.id}/*.fastq:file`

Fastq file

*.fastq

`reads_per_level`

`meta:map`

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

`${meta.id}/reads_per_level.txt:file`

Reads per level

*.txt

`remapped`

`meta:map`

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

`${meta.id}/remapped_with_a.bam*:file`

Remapped BAM file

*.bam*

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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`

`${meta.id}:file`

`extraction`

`meta:map`

`${meta.id}/extraction.bam*:file`

`extraction_mapped`

`meta:map`

`${meta.id}/extraction_mapped.bam:file`

`extraction_unmpapped`

`meta:map`

`${meta.id}/extraction_unmapped.bam:file`

`hla`

`meta:map`

`${meta.id}/hla/*:file`

`fastq`

`meta:map`

`${meta.id}/*.fastq:file`

`reads_per_level`

`meta:map`

`${meta.id}/reads_per_level.txt:file`

`remapped`

`meta:map`

`${meta.id}/remapped_with_a.bam*:file`

`versions`

`versions.yml:file`

Tools

hlala
GPL

maintainer

get in touch

modules/hlala_typing

Description

Input

meta:map

bam:file

bai:file

graph:directory

Output

results

meta:map

${meta.id}:file

extraction

meta:map

${meta.id}/extraction.bam*:file

extraction_mapped

meta:map

${meta.id}/extraction_mapped.bam:file

extraction_unmpapped

meta:map

${meta.id}/extraction_unmapped.bam:file

hla

meta:map

${meta.id}/hla/*:file

fastq

meta:map

${meta.id}/*.fastq:file

reads_per_level

meta:map

${meta.id}/reads_per_level.txt:file

remapped

meta:map

${meta.id}/remapped_with_a.bam*:file

versions

versions.yml:file

Tools

hlala GPL

maintainer

get in touch

`meta:map`

`bam:file`

`bai:file`

`graph:directory`

`results`

`meta:map`

`${meta.id}:file`

`extraction`

`meta:map`

`${meta.id}/extraction.bam*:file`

`extraction_mapped`

`meta:map`

`${meta.id}/extraction_mapped.bam:file`

`extraction_unmpapped`

`meta:map`

`${meta.id}/extraction_unmapped.bam:file`

`hla`

`meta:map`

`${meta.id}/hla/*:file`

`fastq`

`meta:map`

`${meta.id}/*.fastq:file`

`reads_per_level`

`meta:map`

`${meta.id}/reads_per_level.txt:file`

`remapped`

`meta:map`

`${meta.id}/remapped_with_a.bam*:file`

`versions`

`versions.yml:file`

hlala
GPL