modules/sentieon_dedup

Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.

memdedupmapbamcramsentieon

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

Description

Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM file.

*.bam

`bai`
`:file`

BAI file

*.bai

`meta2`
`:map`

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

`fasta`
`:file`

Genome fasta file

*.{fa,fasta}

`meta3`
`: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

`cram`

`meta`
`:map`

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

`*.cram`
`:file`

CRAM file

*.cram

`crai`

`meta`
`:map`

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

`*.crai`
`:file`

CRAM index file

*.crai

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

BAM file.

*.bam

`bai`

`meta`
`:map`

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

`*.bai`
`:file`

BAI file

*.bai

`score`

`meta`
`:map`

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

`*.score`
`:file`

The score file indicates which reads LocusCollector finds are likely duplicates.

*.score

`metrics`

`meta`
`:map`

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

`*.metrics`
`:file`

Output file containing Dedup metrics incl. histogram data.

*.metrics

`metrics_multiqc_tsv`

`meta`
`:map`

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

`*.metrics.multiqc.tsv`
`:file`

Output tsv-file containing Dedup metrics excl. histogram data.

*.metrics.multiqc.tsv

`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

`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_dedup

Description

Input

meta:map

bam:file

bai:file

meta2:map

fasta:file

meta3:map

fasta_fai:file

Output

cram

meta:map

*.cram:file

crai

meta:map

*.crai:file

bam

meta:map

*.bam:file

bai

meta:map

*.bai:file

score

meta:map

*.score:file

metrics

meta:map

*.metrics:file

metrics_multiqc_tsv

meta:map

*.metrics.multiqc.tsv:file

versions_sentieon

${task.process}:string

sentieon:string

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

Topics

versions

${task.process}:string

sentieon:string

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

Tools

sentieon

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fasta_fai`
`:file`

`cram`

`meta`
`:map`

`*.cram`
`:file`

`crai`

`meta`
`:map`

`*.crai`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`score`

`meta`
`:map`

`*.score`
`:file`

`metrics`

`meta`
`:map`

`*.metrics`
`:file`

`metrics_multiqc_tsv`

`meta`
`:map`

`*.metrics.multiqc.tsv`
`:file`

`versions_sentieon`

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

`sentieon`
`:string`

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

`versions`

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

`sentieon`
`:string`

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