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

]

`tumor_bam:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`tumor_bam_index:file`

BAM/CRAM/SAM index file

*.{bai,crai}

`normal_bam:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`normal_bam_index:file`

BAM/CRAM/SAM index file

*.{bai,crai}

`intervals:file`

BED

*.bed

`scan:file`

Input scan file from MSIsensor2 scan module

`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

]

`${prefix}:file`

MSI classifications as a text file

`distribution`

`meta:map`

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

]

`${prefix}_dis:file`

Read count distributions of MSI regions

`somatic`

`meta:map`

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

]

`${prefix}_somatic:file`

Somatic MSI regions detected.

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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`

`normal_bam:file`

`normal_bam_index:file`

`intervals:file`

`scan:file`

`models:file`

Output

`msi`

`meta:map`

`${prefix}:file`

`distribution`

`meta:map`

`${prefix}_dis:file`

`somatic`

`meta:map`

`${prefix}_somatic:file`

`versions`

`versions.yml:file`

Tools

msisensor2

maintainer

get in touch