modules/msisensor2_msi

msisensor2 detection of MSI regions.

msimicrosatellitemicrosatellite instabilitytumorcfDNA

https://github.com/nf-core/modules/[...]/modules/nf-core/msisensor2/msi

Description

msisensor2 detection of MSI regions.

Input

name:type

description

pattern

`meta`
`:map`

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

`tumor_bam`
`:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`tumor_bam_index`
`:file`

BAM/CRAM/SAM index file

*.{bai,crai}

`meta2`
`:map`

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

`models`
`:file`

Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan)

*/*

Output

name:type

description

pattern

`msi`

`meta`
`:map`

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

`${prefix}`
`:file`

MSI classifications as a text file

`distribution`

`meta`
`:map`

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

`${prefix}_dis`
`:file`

Read count distributions of MSI regions

`somatic`

`meta`
`:map`

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

`${prefix}_somatic`
`:file`

Somatic MSI regions detected.

`versions_msisensor2`

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

The name of the process

`msisensor2`
`:string`

The name of the tool

`msisensor2 2> >(grep Version) | sed 's/Version: v//g'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`msisensor2`
`:string`

The name of the tool

`msisensor2 2> >(grep Version) | sed 's/Version: v//g'`
`:eval`

The expression to obtain the version of the tool

Tools

msisensor2

MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.

github.com/niu-lab/msisensor2 github.com/niu-lab/msisensor2/blob/master/README.md https://github.com/niu-lab/msisensor2

modules/msisensor2_msi

Description

Input

`meta`
`:map`

`tumor_bam`
`:file`

`tumor_bam_index`
`:file`

`meta2`
`:map`

`models`
`:file`

Output

`msi`

`meta`
`:map`

`${prefix}`
`:file`

`distribution`

`meta`
`:map`

`${prefix}_dis`
`:file`

`somatic`

`meta`
`:map`

`${prefix}_somatic`
`:file`

`versions_msisensor2`

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

`msisensor2`
`:string`

`msisensor2 2> >(grep Version) | sed 's/Version: v//g'`
`:eval`

Topics

`versions`

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

`msisensor2`
`:string`

`msisensor2 2> >(grep Version) | sed 's/Version: v//g'`
`:eval`

Tools

msisensor2

included in

maintainer

get in touch

modules/msisensor2_msi

Description

Input

meta:map

tumor_bam:file

tumor_bam_index:file

meta2:map

models:file

Output

msi

meta:map

${prefix}:file

distribution

meta:map

${prefix}_dis:file

somatic

meta:map

${prefix}_somatic:file

versions_msisensor2

${task.process}:string

msisensor2:string

msisensor2 2> >(grep Version) | sed 's/Version: v//g':eval

Topics

versions

${task.process}:string

msisensor2:string

msisensor2 2> >(grep Version) | sed 's/Version: v//g':eval

Tools

msisensor2

included in

maintainer

get in touch

`meta`
`:map`

`tumor_bam`
`:file`

`tumor_bam_index`
`:file`

`meta2`
`:map`

`models`
`:file`

`msi`

`meta`
`:map`

`${prefix}`
`:file`

`distribution`

`meta`
`:map`

`${prefix}_dis`
`:file`

`somatic`

`meta`
`:map`

`${prefix}_somatic`
`:file`

`versions_msisensor2`

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

`msisensor2`
`:string`

`msisensor2 2> >(grep Version) | sed 's/Version: v//g'`
`:eval`

`versions`

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

`msisensor2`
`:string`

`msisensor2 2> >(grep Version) | sed 's/Version: v//g'`
`:eval`