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

This module is deprecated.

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_msisensor`

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

The name of the process

`msisensor`
`:string`

The name of the tool

`msisensor 2>&1 | sed -nE 's/Version:\sv([0-9]\.[0-9])/\1/ p'`
`:string`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`msisensor`
`:string`

The name of the tool

`msisensor 2>&1 | sed -nE 's/Version:\sv([0-9]\.[0-9])/\1/ p'`
`:string`

The expression to obtain the version of the tool

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_msisensor`

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

`msisensor`
`:string`

`msisensor 2>&1 | sed -nE 's/Version:\sv([0-9]\.[0-9])/\1/ p'`
`:string`

Topics

`versions`

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

`msisensor`
`:string`

`msisensor 2>&1 | sed -nE 's/Version:\sv([0-9]\.[0-9])/\1/ p'`
`:string`

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_msisensor

${task.process} :string

msisensor :string

msisensor 2>&1 | sed -nE 's/Version:\sv([0-9]\.[0-9])/\1/ p' :string

Topics

versions

${task.process} :string

msisensor :string

msisensor 2>&1 | sed -nE 's/Version:\sv([0-9]\.[0-9])/\1/ p' :string

Tools

msisensorMIT

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_msisensor`

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

`msisensor`
`:string`

`msisensor 2>&1 | sed -nE 's/Version:\sv([0-9]\.[0-9])/\1/ p'`
`:string`

`versions`

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

`msisensor`
`:string`

`msisensor 2>&1 | sed -nE 's/Version:\sv([0-9]\.[0-9])/\1/ p'`
`:string`

msisensor
MIT