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 (map)

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

]

reads (file)

fastq.gz files

*.fastq.gz

interval_file (file)

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

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

meta2 (map)

Groovy Map containing fasta information

fasta (file)

reference fasta file - must be unzipped

*.fasta

meta3 (map)

Groovy Map containing index information

index (file)

reference BWA index

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

known_sites (file)

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

*.vcf.gz

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bam (file)

Sorted BAM file

*.bam

bai (file)

index corresponding to sorted BAM file

*.bai

qc_metrics (directory)

(optional) optional directory of qc metrics

qc_metrics

bqsr_table (file)

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

*.table

duplicate_metrics (file)

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

*-duplicate-metrics.txt
maintainers
Github user bsiranosian
Github user adamrtalbot
get in touch
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Tools

parabricks
custom

NVIDIA Clara Parabricks GPU-accelerated genomics tools

nvidia.com/en-us/clara/genomics docs.nvidia.com/clara/parabricks/4.0.1/Documentation