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nf-core/parabricks/minimap2 @ 0.0.0-0c7146d

NVIDIA Clara Parabricks GPU-accelerated minimap2 for aligning long read sequences against a large reference database using an accelerated KSW2 to convert FASTQ to BAM/CRAM.

align sort bqsr duplicates long read
Latest version: 0.0.0-0c7146d
Total downloads: 3
Source: nf-core/modules
Authors: @haidyi
Maintainers: @haidyi

Summary

NVIDIA Clara Parabricks GPU-accelerated minimap2 for aligning long read sequences against a large reference database using an accelerated KSW2 to convert FASTQ to BAM/CRAM.

Get started

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

include { PARABRICKS_MINIMAP2 } from 'nf-core/parabricks/minimap2'

License

MIT License

Process
Name PARABRICKS_MINIMAP2
Input 5 channels
#1 tuple
meta map

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

Input read file, supported formats - 'fastq', 'fastq.gz', 'fq', 'fq.gz', 'bam'

 ^.*\.(fastq|fastq\.gz|fq|fq\.gz|bam)$
#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
intervals file

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

 *.{bed,interval_list,picard,list,intervals}
#4 tuple
meta4 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 ]
*.duplicate-metrics.txt file

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

 *.duplicate-metrics.txt
#8 compatible_versions
compatible_versions.yml file

File containing info on compatible CPU-based software versions.

 compatible_versions.yml
#9