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’ ]

`results:file`

Results file

`extraction`

`meta:map`

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

`results/extraction.bam:file`

Extraction BAM file

*.bam

`extraction_index`

`meta:map`

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

`results/extraction.bam.bai:file`

Extraction BAM index file

*.bam.bai

`extraction_mapped`

`meta:map`

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

`results/extraction_mapped.bam:file`

Extraction mapped BAM file

*.bam

`extraction_unmpapped`

`meta:map`

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

`results/extraction_unmapped.bam:file`

Extraction unmapped BAM file

*.bam

`hla`

`meta:map`

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

`results/hla/*:file`

HLA results

`fastq`

`meta:map`

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

`results/*.fastq:file`

Fastq file

*.fastq

`reads_per_level`

`meta:map`

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

`results/reads_per_level.txt:file`

Reads per level

*.txt

`remapped`

`meta:map`

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

`results/remapped_with_a.bam:file`

Remapped BAM file

*.bam

`remapped_index`

`meta:map`

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

`results/remapped_with_a.bam.bai:file`

Remapped BAM index file

*.bam.bai

`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

results:file

extraction

meta:map

results/extraction.bam:file

extraction_index

meta:map

results/extraction.bam.bai:file

extraction_mapped

meta:map

results/extraction_mapped.bam:file

extraction_unmpapped

meta:map

results/extraction_unmapped.bam:file

hla

meta:map

results/hla/*:file

fastq

meta:map

results/*.fastq:file

reads_per_level

meta:map

results/reads_per_level.txt:file

remapped

meta:map

results/remapped_with_a.bam:file

remapped_index

meta:map

results/remapped_with_a.bam.bai:file

versions

versions.yml:file

Tools

hlala GPL

`meta:map`

`bam:file`

`bai:file`

`graph:directory`

`results`

`meta:map`

`results:file`

`extraction`

`meta:map`

`results/extraction.bam:file`

`extraction_index`

`meta:map`

`results/extraction.bam.bai:file`

`extraction_mapped`

`meta:map`

`results/extraction_mapped.bam:file`

`extraction_unmpapped`

`meta:map`

`results/extraction_unmapped.bam:file`

`hla`

`meta:map`

`results/hla/*:file`

`fastq`

`meta:map`

`results/*.fastq:file`

`reads_per_level`

`meta:map`

`results/reads_per_level.txt:file`

`remapped`

`meta:map`

`results/remapped_with_a.bam:file`

`remapped_index`

`meta:map`

`results/remapped_with_a.bam.bai:file`

`versions`

`versions.yml:file`

hlala
GPL