modules/parabricks_fq2bam

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.

alignsortbqsrduplicates

https://github.com/nf-core/modules/[...]/modules/nf-core/parabricks/fq2bam

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:false ]

`reads:file`

fastq.gz files

*.fastq.gz

`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}

`meta4:map`

Groovy Map containing index information

`interval_file:file`

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

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

`meta5:map`

Groovy Map containing known sites information

`known_sites:file`

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

*.vcf.gz

`output_fmt:string`

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

{bam,cram}

Output

name:type

description

pattern

`bam`

`meta:map`

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

`*.bam:file`

Sorted BAM file

*.bam

`bai`

`meta:map`

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

`*.bai:file`

index corresponding to sorted BAM file

*.bai

`cram`

`meta:map`

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

`*.cram:file`

Sorted CRAM file

*.cram

`crai`

`meta:map`

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

`*.crai:file`

index corresponding to sorted CRAM file

*.crai

`bqsr_table`

`meta:map`

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

`*.table:file`

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

*.table

`qc_metrics`

`meta:map`

Groovy Map containing sample information

`*_qc_metrics:directory`

(optional) optional directory of qc metrics

*_qc_metrics

`duplicate_metrics`

`meta:map`

Groovy Map containing sample information

`*.duplicate-metrics.txt:file`

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

*.duplicate-metrics.txt

`versions`

`versions.yml: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

modules/parabricks_fq2bam

Description

Input

meta:map

reads:file

meta2:map

fasta:file

meta3:map

index:file

meta4:map

interval_file:file

meta5:map

known_sites:file

output_fmt:string

Output

bam

meta:map

*.bam:file

bai

meta:map

*.bai:file

cram

meta:map

*.cram:file

crai

meta:map

*.crai:file

bqsr_table

meta:map

*.table:file

qc_metrics

meta:map

*_qc_metrics:directory

duplicate_metrics

meta:map

*.duplicate-metrics.txt:file

versions

versions.yml:file

Tools

parabricks custom

`meta:map`

`reads:file`

`meta2:map`

`fasta:file`

`meta3:map`

`index:file`

`meta4:map`

`interval_file:file`

`meta5:map`

`known_sites:file`

`output_fmt:string`

`bam`

`meta:map`

`*.bam:file`

`bai`

`meta:map`

`*.bai:file`

`cram`

`meta:map`

`*.cram:file`

`crai`

`meta:map`

`*.crai:file`

`bqsr_table`

`meta:map`

`*.table:file`

`qc_metrics`

`meta:map`

`*_qc_metrics:directory`

`duplicate_metrics`

`meta:map`

`*.duplicate-metrics.txt:file`

`versions`

`versions.yml:file`

parabricks
custom