modules/sentieon_bwamem

Performs fastq alignment to a fasta reference using Sentieon’s BWA MEM

membwaalignmentmapfastqbamsentieon

https://github.com/nf-core/modules/[...]/modules/nf-core/sentieon/bwamem

Description

Performs fastq alignment to a fasta reference using Sentieon’s BWA MEM

Input

name:type

description

pattern

`meta:map`

Groovy Map containing reference information. e.g. [ id:‘test’, single_end

]

`reads:file`

Genome fastq files (single-end or paired-end)

`meta2:map`

Groovy Map containing reference information. e.g. [ id:‘test’, single_end

]

`index:file`

BWA genome index files

*.{amb,ann,bwt,pac,sa}

`meta3:map`

Groovy Map containing reference information. e.g. [ id:‘test’, single_end

]

`fasta:file`

Genome fasta file

*.{fa,fasta}

`meta4:map`

Groovy Map containing reference information. e.g. [ id:‘test’, single_end

]

`fasta_fai:file`

The index of the FASTA reference.

*.fai

Output

name:type

description

pattern

`bam_and_bai`

`meta:map`

Groovy Map containing reference information. e.g. [ id:‘test’, single_end

]

`${prefix}:file`

BAM file with corresponding index.

*.{bam,bai}

`${prefix}.{bai,crai}:file`

BAM file with corresponding index.

*.{bam,bai}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

sentieon

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon.com

modules/sentieon_bwamem

Description

Input

`meta:map`

`reads:file`

`meta2:map`

`index:file`

`meta3:map`

`fasta:file`

`meta4:map`

`fasta_fai:file`

Output

`bam_and_bai`

`meta:map`

`${prefix}:file`

`${prefix}.{bai,crai}:file`

`versions`

`versions.yml:file`

Tools

sentieon

included in

maintainers

get in touch