modules/msisensor_msi

Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data

homoploymermicrosatelliteMSIinstability

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

Description

Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data

Input

name:type

description

pattern

`meta`
`:map`

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

`normal_bam`
`:file`

Coordinate sorted BAM/CRAM/SAM file from normal tissue

*.{bam,cram,sam}

`normal_bai`
`:file`

Index for coordinate sorted BAM/CRAM/SAM file from normal tissue

*.{bam,cram,sam}

`tumor_bam`
`:file`

Coordinate sorted BAM/CRAM/SAM file from tumor tissue

*.{bam,cram,sam}

`tumor_bai`
`:file`

Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue

*.{bam,cram,sam}

`metascan`
`:file`

metascan file

`homopolymers`
`:file`

Output file from MSIsensor scan module

*.msisensor_scan.tab

Output

name:type

description

pattern

`output`

`meta`
`:map`

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

`${prefix}`
`:file`

Output file from MSIsensor msi module

`output_dis`

`meta`
`:map`

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

`${prefix}_dis`
`:file`

Output file from MSIsensor module

`output_germline`

`meta`
`:map`

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

`${prefix}_germline`
`:file`

Output file from MSIsensor module

`output_somatic`

`meta`
`:map`

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

`${prefix}_somatic`
`:file`

Output file from MSIsensor module

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

msisensor
MIT

MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.

github.com/ding-lab/msisensor 10.1093/bioinformatics/btt755

modules/msisensor_msi

Description

Input

`meta`
`:map`

`normal_bam`
`:file`

`normal_bai`
`:file`

`tumor_bam`
`:file`

`tumor_bai`
`:file`

`metascan`
`:file`

`homopolymers`
`:file`

Output

`output`

`meta`
`:map`

`${prefix}`
`:file`

`output_dis`

`meta`
`:map`

`${prefix}_dis`
`:file`

`output_germline`

`meta`
`:map`

`${prefix}_germline`
`:file`

`output_somatic`

`meta`
`:map`

`${prefix}_somatic`
`:file`

`versions`

`versions.yml`
`:file`

Tools

msisensor
MIT

maintainer

get in touch

modules/msisensor_msi

Description

Input

meta:map

normal_bam:file

normal_bai:file

tumor_bam:file

tumor_bai:file

metascan:file

homopolymers:file

Output

output

meta:map

${prefix}:file

output_dis

meta:map

${prefix}_dis:file

output_germline

meta:map

${prefix}_germline:file

output_somatic

meta:map

${prefix}_somatic:file

versions

versions.yml:file

Tools

msisensor MIT

maintainer

get in touch

`meta`
`:map`

`normal_bam`
`:file`

`normal_bai`
`:file`

`tumor_bam`
`:file`

`tumor_bai`
`:file`

`metascan`
`:file`

`homopolymers`
`:file`

`output`

`meta`
`:map`

`${prefix}`
`:file`

`output_dis`

`meta`
`:map`

`${prefix}_dis`
`:file`

`output_germline`

`meta`
`:map`

`${prefix}_germline`
`:file`

`output_somatic`

`meta`
`:map`

`${prefix}_somatic`
`:file`

`versions`

`versions.yml`
`:file`

msisensor
MIT