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:false ]

`reads`
`:file`

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

`meta2`
`:map`

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

`index`
`:file`

BWA genome index files

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

`meta3`
`:map`

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

`fasta`
`:file`

Genome fasta file

*.{fa,fasta}

`meta4`
`:map`

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

`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:false ]

`${prefix}`
`:file`

BAM file with corresponding index.

*.{bam,bai}

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

BAM file with corresponding index.

*.{bam,bai}

`versions_bwa`

`${task.process}`
`:string`

The process the versions were collected from

`bwa`
`:string`

The tool name

`sentieon bwa 2>&1 | sed -n "s/^Version: *//p"`
`:string`

The command used to generate the version of the tool

`versions_sentieon`

`${task.process}`
`:string`

The process the versions were collected from

`sentieon`
`:string`

The tool name

`sentieon driver --version | sed "s/.*-//g"`
`:string`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`bwa`
`:string`

The tool name

`sentieon bwa 2>&1 | sed -n "s/^Version: *//p"`
`:string`

The command used to generate the version of the tool

`${task.process}`
`:string`

The process the versions were collected from

`sentieon`
`:string`

The tool name

`sentieon driver --version | sed "s/.*-//g"`
`: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

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_bwa`

`${task.process}`
`:string`

`bwa`
`:string`

`sentieon bwa 2>&1 | sed -n "s/^Version: *//p"`
`:string`

`versions_sentieon`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

Topics

`versions`

`${task.process}`
`:string`

`bwa`
`:string`

`sentieon bwa 2>&1 | sed -n "s/^Version: *//p"`
`:string`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

Tools

sentieon

included in

maintainers

get in touch

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_bwa

${task.process}:string

bwa:string

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

versions_sentieon

${task.process}:string

sentieon:string

sentieon driver --version | sed "s/.*-//g":string

Topics

versions

${task.process}:string

bwa:string

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

${task.process}:string

sentieon:string

sentieon driver --version | sed "s/.*-//g":string

Tools

sentieon

included in

maintainers

get in touch

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`index`
`:file`

`meta3`
`:map`

`fasta`
`:file`

`meta4`
`:map`

`fasta_fai`
`:file`

`bam_and_bai`

`meta`
`:map`

`${prefix}`
`:file`

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

`versions_bwa`

`${task.process}`
`:string`

`bwa`
`:string`

`sentieon bwa 2>&1 | sed -n "s/^Version: *//p"`
`:string`

`versions_sentieon`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

`versions`

`${task.process}`
`:string`

`bwa`
`:string`

`sentieon bwa 2>&1 | sed -n "s/^Version: *//p"`
`:string`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`