modules/msisensorpro_msisomatic

MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input

micro-satellite-scanmsisensor-promsisomatic

https://github.com/nf-core/modules/[...]/modules/nf-core/msisensorpro/msisomatic

Description

Input

name:type

description

pattern

`meta:map`

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

]

`normal:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`normal_index:file`

BAM/CRAM/SAM index file

*.{bai,crai,sai}

`tumor:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`tumor_index:file`

BAM/CRAM/SAM index file

*.{bai,crai,sai}

`intervals:file`

bed file containing interval information, optional

*.{bed}

`fasta:file`

Reference genome

*.{fasta}

`msisensor_scan:file`

Output from msisensor-pro/scan, containing list of msi regions

*.list

Output

name:type

description

pattern

`output_report`

`meta:map`

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

]

`${prefix}:file`

File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score

`output_dis`

`meta:map`

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

]

`${prefix}_dis:file`

File containing distribution results

`output_germline`

`meta:map`

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

]

`${prefix}_germline:file`

File containing germline results

`output_somatic`

`meta:map`

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

]

`${prefix}_somatic:file`

File containing somatic results

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

msisensorpro
Custom Licence

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

github.com/xjtu-omics/msisensor-pro github.com/xjtu-omics/msisensor-pro/wiki https://github.com/xjtu-omics/msisensor-pro 10.1016/j.gpb.2020.02.001

modules/msisensorpro_msisomatic

Description

Input

`meta:map`

`normal:file`

`normal_index:file`

`tumor:file`

`tumor_index:file`

`intervals:file`

`fasta:file`

`msisensor_scan:file`

Output

`output_report`

`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

msisensorpro
Custom Licence

included in

maintainer

get in touch

modules/msisensorpro_msisomatic

Description

Input

meta:map

normal:file

normal_index:file

tumor:file

tumor_index:file

intervals:file

fasta:file

msisensor_scan:file

Output

output_report

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

msisensorpro Custom Licence

included in

maintainer

get in touch

`meta:map`

`normal:file`

`normal_index:file`

`tumor:file`

`tumor_index:file`

`intervals:file`

`fasta:file`

`msisensor_scan:file`

`output_report`

`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`

msisensorpro
Custom Licence