Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

:file

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

meta2{:bash}

:map

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

index{:bash}

:file

BWA genome index files

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

meta3{:bash}

:map

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

fasta{:bash}

:file

Genome fasta file

*.{fa,fasta}

meta4{:bash}

:map

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

fasta_fai{:bash}

:file

The index of the FASTA reference.

*.fai

Output

name:type
description
pattern

bam_and_bai{:bash}

meta{:bash}

:map

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

${prefix}{:bash}

:file

BAM file with corresponding index.

*.{bam,bai}

${prefix}.{bai,crai}{:bash}

:file

BAM file with corresponding index.

*.{bam,bai}

versions_bwa{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

bwa{:bash}

:string

The tool name

sentieon bwa 2>&1 | sed -n "s/^Version: *//p"{:bash}

:string

The command used to generate the version of the tool

versions_sentieon{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

sentieon{:bash}

:string

The tool name

sentieon driver --version | sed "s/.*-//g"{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

bwa{:bash}

:string

The tool name

sentieon bwa 2>&1 | sed -n "s/^Version: *//p"{:bash}

:string

The command used to generate the version of the tool

${task.process}{:bash}

:string

The process the versions were collected from

sentieon{:bash}

:string

The tool name

sentieon driver --version | sed "s/.*-//g"{:bash}

:string

The command used to generate the version of the tool

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
included in
rarediseasesarek
maintainers
Github user asp8200
Github user DonFreed
get in touch
Ask a question on Slack Open an issue on GitHub