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

]

`bam:file`

BAM file.

*.bam

`bai:file`

BAI file

*.bai

`meta2:map`

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

]

`fasta:file`

Genome fasta file

*.{fa,fasta}

`meta3: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

`cram`

`meta:map`

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

]

`*.cram:file`

CRAM file

*.cram

`crai`

`meta:map`

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

]

`*.crai:file`

CRAM index file

*.crai

`bam`

`meta:map`

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

]

`*.bam:file`

BAM file.

*.bam

`bai`

`meta:map`

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

]

`*.bai:file`

BAI file

*.bai

`score`

`meta:map`

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

]

`*.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

]

`*.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

]

`*.metrics.multiqc.tsv:file`

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

*.metrics.multiqc.tsv

`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_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`

`versions.yml:file`

Tools

sentieon

included in

maintainer

get in touch