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{:bash}

:map

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

bam{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

bai{:bash}

:file

BAM index file

*.{bai}

graph{:bash}

:directory

Path to prepared graph with hla-la —action prepareGraph

Output

name:type
description
pattern

results{:bash}

meta{:bash}

:map

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

results{:bash}

:file

Results file

extraction{:bash}

meta{:bash}

:map

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

results/extraction.bam{:bash}

:file

Extraction BAM file

*.bam

extraction_index{:bash}

meta{:bash}

:map

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

results/extraction.bam.bai{:bash}

:file

Extraction BAM index file

*.bam.bai

extraction_mapped{:bash}

meta{:bash}

:map

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

results/extraction_mapped.bam{:bash}

:file

Extraction mapped BAM file

*.bam

extraction_unmpapped{:bash}

meta{:bash}

:map

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

results/extraction_unmapped.bam{:bash}

:file

Extraction unmapped BAM file

*.bam

hla{:bash}

meta{:bash}

:map

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

results/hla/*{:bash}

:file

HLA results

fastq{:bash}

meta{:bash}

:map

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

results/*.fastq{:bash}

:file

Fastq file

*.fastq

reads_per_level{:bash}

meta{:bash}

:map

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

results/reads_per_level.txt{:bash}

:file

Reads per level

*.txt

remapped{:bash}

meta{:bash}

:map

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

results/remapped_with_a.bam{:bash}

:file

Remapped BAM file

*.bam

remapped_index{:bash}

meta{:bash}

:map

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

results/remapped_with_a.bam.bai{:bash}

:file

Remapped BAM index file

*.bam.bai

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user mapo9
get in touch
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