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nf-core/parabricks/fq2bammeth @ 0.0.0-0c7146d

NVIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence

align sort bqsr duplicates bwameth
Latest version: 0.0.0-0c7146d
Total downloads: 4
Source: nf-core/modules
Authors: @sateeshperi
Maintainers: @sateeshperi @gallvp

Summary

NVIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence

Get started

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

include { PARABRICKS_FQ2BAMMETH } from 'nf-core/parabricks/fq2bammeth'

License

MIT License

Process
Name PARABRICKS_FQ2BAMMETH
Input 4 channels
#1 tuple
meta map

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

fastq.gz files

 *.fastq.gz
#2 tuple
meta2 map

Groovy Map containing fasta information
fasta file

reference fasta file - must be unzipped

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

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

index corresponding to sorted BAM file

 *.bai
#2 bam tuple
meta map

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

Sorted BAM file

 *.bam
#3 bqsr_table
*.table file

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

 *.table
#4 qc_metrics
qc_metrics directory

(optional) optional directory of qc metrics

 qc_metrics
#5 duplicate_metrics
duplicate-metrics.txt file

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

 *-duplicate-metrics.txt
#6 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 19:24:02 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fparabricks%2Ffq2bammeth/0.0.0-0c7146d/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/parabricks/fq2bammeth/blobs/sha256:2d7dd6e528376c0dcc69c6974e1964b186725c2a5177e89fbe3a9f535df11664
Size 3.6 KB
Checksum sha256:2d7dd6e528376c0dcc69c6974e1964b186725c2a5177e89fbe3a9f535df11664