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nf-core/parabricks/applybqsr @ 0.0.0-0c7146d

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

bqsr bam GPU-accelerated base quality score recalibration
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @bsiranosian
Maintainers: @bsiranosian @famosab

Summary

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

Get started

Add the following snippet to your workflow script to include this module.

include { PARABRICKS_APPLYBQSR } from 'nf-core/parabricks/applybqsr'

License

MIT License

Process
Name PARABRICKS_APPLYBQSR
Input 5 channels
#1 tuple
meta map

Groovy Map containing sample information. e.g. [ id:'test' ]
bam file

BAM file

 *.bam
#2 tuple
meta2 map

Groovy Map containing sample information. e.g. [ id:'test' ]
bam_index file

BAM index file

 *.bam.bai
#3 tuple
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
#4 tuple
meta4 map

Groovy Map containing sample information. e.g. [ id:'test' ]
intervals file

intervals
#5 tuple
meta5 map

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

Reference fasta - must be unzipped.

 *.fasta
Output 3 channels
#1 bai tuple
meta map

Groovy Map containing sample information. e.g. [ id:'test' ]
*.bai file

bai index corresponding to output bam file.

 *.bam.bai
#2 bam tuple
meta map

Groovy Map containing sample information. e.g. [ id:'test' ]
*.bam file

BAM file after applying BQSR.

 *.bam
#3 versions_parabricks tuple
${task.process} string

The process the versions were collected from
parabricks string

The tool name
pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//' string

The command used to generate the version of the tool
Tool Description Homepage
parabricks NVIDIA Clara Parabricks GPU-accelerated genomics tools https://www.nvidia.com/en-us/clara/genomics/
Version 0.0.0-0c7146d
Commit ID 0c7146d85582628b5d1034504702fa808632b1af
Release Date 08 Apr 2026 19:00:58 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fparabricks%2Fapplybqsr/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/parabricks/applybqsr/blobs/sha256:212efc8ce47b792dd324e5abd53446f629373aed4af7afeea9029e29453d1b42
Size 3.0 KB
Checksum sha256:212efc8ce47b792dd324e5abd53446f629373aed4af7afeea9029e29453d1b42
Downloads 1
Version Date Status Downloads Size Diff
0.0.0-0c7146d