Description

NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked.

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

:file

fastq.gz files

*.fastq.gz

meta2{:bash}

:map

Groovy Map containing fasta information

fasta{:bash}

:file

reference fasta file - must be unzipped

*.fasta

meta3{:bash}

:map

Groovy Map containing index information

index{:bash}

:file

reference BWA index

*.{amb,ann,bwt,pac,sa}

meta4{:bash}

:map

Groovy Map containing index information

interval_file{:bash}

:file

(optional) file(s) containing genomic intervals for use in base quality score recalibration (BQSR)

*.{bed,interval_list,picard,list,intervals}

meta5{:bash}

:map

Groovy Map containing known sites information

known_sites{:bash}

:file

(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.

*.vcf.gz

output_fmt{:bash}

:string

Output format for the alignment. Options are ‘bam’ or ‘cram’

{bam,cram}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

Sorted BAM file

*.bam

bai{:bash}

meta{:bash}

:map

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

*.bai{:bash}

:file

index corresponding to sorted BAM file

*.bai

cram{:bash}

meta{:bash}

:map

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

*.cram{:bash}

:file

Sorted CRAM file

*.cram

crai{:bash}

meta{:bash}

:map

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

*.crai{:bash}

:file

index corresponding to sorted CRAM file

*.crai

bqsr_table{:bash}

meta{:bash}

:map

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

*.table{:bash}

:file

(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr

*.table

qc_metrics{:bash}

meta{:bash}

:map

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

*_qc_metrics{:bash}

:directory

(optional) optional directory of qc metrics

*_qc_metrics

duplicate_metrics{:bash}

meta{:bash}

:map

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

*.duplicate-metrics.txt{:bash}

:file

(optional) metrics calculated from marking duplicates in the bam file

*.duplicate-metrics.txt

compatible_versions{:bash}

compatible_versions.yml{:bash}

:file

File containing info on compatible CPU-based software versions.

compatible_versions.yml

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

parabricks
custom

NVIDIA Clara Parabricks GPU-accelerated genomics tools

nvidia.com/en-us/clara/genomics docs.nvidia.com/clara/parabricks/latest
included in
sarek
maintainers
Github user bsiranosian
Github user adamrtalbot
Github user gallvp
Github user famosab
get in touch
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