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nf-core/parabricks/fq2bam @ 0.0.0-0c7146d

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.

align sort bqsr duplicates
Latest version: 0.0.0-0c7146d
Total downloads: 3
Source: nf-core/modules
Authors: @bsiranosian @adamrtalbot
Maintainers: @bsiranosian @adamrtalbot @gallvp @famosab

Summary

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.

Get started

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

include { PARABRICKS_FQ2BAM } from 'nf-core/parabricks/fq2bam'

License

MIT License

Process
Name PARABRICKS_FQ2BAM
Input 6 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}
#4 tuple
meta4 map

Groovy Map containing index information
intervals file

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

 *.{bed,interval_list,picard,list,intervals}
#5 tuple
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 9 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 crai tuple
meta map

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

index corresponding to sorted CRAM file

 *.crai
#4 cram tuple
meta map

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

Sorted CRAM file

 *.cram
#5 bqsr_table tuple
meta map

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

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

 *.table
#6 qc_metrics tuple
meta map

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

(optional) optional directory of qc metrics

 *_qc_metrics
#7 duplicate_metrics tuple
meta map

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