modules/sentieon_readwriter

Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.

mergeconvertreadwritersentieon

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

Description

Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM file.

*.{bam,cram}

`index`
`:file`

BAI/CRAI file.

*.{bai,crai}

`meta2`
`:map`

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

`fasta`
`:file`

Genome fasta file

*.{fa,fasta}

`meta3`
`:map`

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

`fai`
`:file`

The index of the FASTA reference.

*.fai

Output

name:type

description

pattern

`output`

`meta`
`:map`

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

`${prefix}`
`:file`

BAM/CRAM file. Depends on how ext.prefix is set. BAM “ext.prefix = .bam”, CRAM “ext.prefix = .cram”. Defaults to cram

*.{bam,cram}

`index`

`meta`
`:map`

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

`${prefix}.${index}`
`:file`

BAM/CRAM index file

*.{bai,crai}

`output_index`

`meta`
`:map`

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

`${prefix}`
`:file`

BAM/CRAM file. Depends on how ext.prefix is set. BAM “ext.prefix = .bam”, CRAM “ext.prefix = .cram”. Defaults to cram

*.{bam,cram}

`${prefix}.${index}`
`:file`

BAM/CRAM index file

*.{bai,crai}

`versions_sentieon`

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

The process the versions were collected from

`sentieon`
`:string`

The tool name

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

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

`sentieon`
`:string`

The tool name

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

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_readwriter

Description

Input

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

Output

`output`

`meta`
`:map`

`${prefix}`
`:file`

`index`

`meta`
`:map`

`${prefix}.${index}`
`:file`

`output_index`

`meta`
`:map`

`${prefix}`
`:file`

`${prefix}.${index}`
`:file`

`versions_sentieon`

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

`sentieon`
`:string`

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

Topics

`versions`

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

`sentieon`
`:string`

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

Tools

sentieon

included in

maintainer

get in touch

modules/sentieon_readwriter

Description

Input

meta :map

input :file

index :file

meta2 :map

fasta :file

meta3 :map

fai :file

Output

output

meta :map

${prefix} :file

index

meta :map

${prefix}.${index} :file

output_index

meta :map

${prefix} :file

${prefix}.${index} :file

versions_sentieon

${task.process} :string

sentieon :string

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

Topics

versions

${task.process} :string

sentieon :string

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

Tools

sentieon

included in

maintainer

get in touch

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`output`

`meta`
`:map`

`${prefix}`
`:file`

`index`

`meta`
`:map`

`${prefix}.${index}`
`:file`

`output_index`

`meta`
`:map`

`${prefix}`
`:file`

`${prefix}.${index}`
`:file`

`versions_sentieon`

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

`sentieon`
`:string`

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

`versions`

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

`sentieon`
`:string`

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