Description

Calculates polymorphic site rates over protein coding genes

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM file

*.bam

bai{:bash}

:file

BAM index file

*.bai

gff{:bash}

:file

GFF file used to extract protein-coding genes

*.gff

fasta{:bash}

:file

Optional fasta file to run on a subset of references in the BAM file.

.{fa,fasta,fas,fna}

Output

name:type
description
pattern

polymut{:bash}

meta{:bash}

:map

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

*.txt{:bash}

:file

Polymut report in .txt format.

*.txt

versions_cmseq{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

cmseq{:bash}

:string

The tool name

VERSION{:bash}

:string

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

cmseq{:bash}

:string

The tool name

VERSION{:bash}

:string

The expression to obtain the version of the tool

Tools

cmseq
MIT License

Set of utilities on sequences and BAM files

github.com/SegataLab/cmseq
maintainer
Github user maxibor
get in touch
Ask a question on Slack Open an issue on GitHub