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

]

`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}

`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

`bam`

`meta:map`

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

]

`*.bam:file`

Sorted BAM file

*.bam

`bai`

`meta:map`

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

]

`*.bai:file`

index corresponding to sorted BAM file

*.bai

`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

`versions`

`versions.yml:file`

File containing software versions

versions.yml

`qc_metrics`

`qc_metrics:directory`

(optional) optional directory of qc metrics

qc_metrics

`duplicate_metrics`

`duplicate-metrics.txt:file`

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

*-duplicate-metrics.txt

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

modules/parabricks_fq2bam

Description

Input

`meta:map`

`reads:file`

`meta2:map`

`fasta:file`

`meta3:map`

`index:file`

`meta4:map`

`interval_file:file`

`known_sites:file`

Output

`bam`

`meta:map`

`*.bam:file`

`bai`

`meta:map`

`*.bai:file`

`bqsr_table`

`meta:map`

`*.table:file`

`versions`

`versions.yml:file`

`qc_metrics`

`qc_metrics:directory`

`duplicate_metrics`

`duplicate-metrics.txt:file`

Tools

parabricks
custom

maintainers

get in touch

modules/parabricks_fq2bam

Description

Input

meta:map

reads:file

meta2:map

fasta:file

meta3:map

index:file

meta4:map

interval_file:file

known_sites:file

Output

bam

meta:map

*.bam:file

bai

meta:map

*.bai:file

bqsr_table

meta:map

*.table:file

versions

versions.yml:file

qc_metrics

qc_metrics:directory

duplicate_metrics

duplicate-metrics.txt:file

Tools

parabricks custom

maintainers

get in touch

`meta:map`

`reads:file`

`meta2:map`

`fasta:file`

`meta3:map`

`index:file`

`meta4:map`

`interval_file:file`

`known_sites:file`

`bam`

`meta:map`

`*.bam:file`

`bai`

`meta:map`

`*.bai:file`

`bqsr_table`

`meta:map`

`*.table:file`

`versions`

`versions.yml:file`

`qc_metrics`

`qc_metrics:directory`

`duplicate_metrics`

`duplicate-metrics.txt:file`

parabricks
custom