Nextflow Registry | nf-core/sentieon/dedup@0.0.0-6c4ed3a

nf-core/sentieon/dedup @ 0.0.0-6c4ed3a

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.

mem dedup map bam cram sentieon

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @asp8200

Maintainers: @asp8200

Summary

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.

Get started

Add the following snippet to your workflow script to include this module.

include { SENTIEON_DEDUP } from 'nf-core/sentieon/dedup'

License

MIT License

Process

`Name`	`SENTIEON_DEDUP`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`bam` file	BAM file. `*.bam`
`bai` file	BAI file `*.bai`

#2 tuple

`meta2` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`fasta` file	Genome fasta file `*.{fa,fasta}`

#3 tuple

`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 8 channels

#1 bai tuple

`meta` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`*.bai` file	BAI file `*.bai`

#2 bam tuple

`meta` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`*.bam` file	BAM file. `*.bam`

#3 crai tuple

`meta` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`*.crai` file	CRAM index file `*.crai`

#4 cram tuple

`meta` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`*.cram` file	CRAM file `*.cram`

#5 score tuple

`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`

#6 metrics tuple

`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`

#7 versions_sentieon tuple

`${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

#8 metrics_multiqc_tsv tuple

`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`

Tool	Description	Homepage
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.