modules/parabricks_applybqsr

NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration (BQSR).

bqsrbamGPU-acceleratedbase quality score recalibration

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

Description

NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration (BQSR).

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM file

*.bam

`meta2`
`:map`

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

`bam_index`
`:file`

BAM index file

*.bam.bai

`meta3`
`:map`

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

`bqsr_table`
`:file`

Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator.

*.table

`meta4`
`:map`

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

`intervals`
`:file`

intervals

`meta5`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`fasta`
`:file`

Reference fasta - must be unzipped.

*.fasta

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

BAM file after applying BQSR.

*.bam

`bai`

`meta`
`:map`

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

`*.bai`
`:file`

bai index corresponding to output bam file.

*.bam.bai

`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_applybqsr

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`bam_index`
`:file`

`meta3`
`:map`

`bqsr_table`
`:file`

`meta4`
`:map`

`intervals`
`:file`

`meta5`
`:map`

`fasta`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`versions`

`versions.yml`
`:file`

Tools

parabricks
custom

maintainers

get in touch

modules/parabricks_applybqsr

Description

Input

meta:map

bam:file

meta2:map

bam_index:file

meta3:map

bqsr_table:file

meta4:map

intervals:file

meta5:map

fasta:file

Output

bam

meta:map

*.bam:file

bai

meta:map

*.bai:file

versions

versions.yml:file

Tools

parabricks custom

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`bam_index`
`:file`

`meta3`
`:map`

`bqsr_table`
`:file`

`meta4`
`:map`

`intervals`
`:file`

`meta5`
`:map`

`fasta`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`versions`

`versions.yml`
`:file`

parabricks
custom