Description

Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

Fasta of list of fasta files recommended to be gathered via with .collect() of bins

*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}

extension{:bash}

:string

Fasta file extension (fa | fas | fasta | …), without .gz suffix, if gzipped input.

Output

name:type
description
pattern

fastatocontig2bin{:bash}

meta{:bash}

:map

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

*.tsv{:bash}

:file

tabular contig2bin file for DAS tool input

*.tsv

versions_dastool{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

dastool{:bash}

:string

The tool name

DAS_Tool --version 2>&1 | grep "DAS Tool" | sed "s/DAS Tool //"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

dastool{:bash}

:string

The name of the tool

DAS_Tool --version 2>&1 | grep "DAS Tool" | sed "s/DAS Tool //"{:bash}

:eval

The expression to obtain the version of the tool

Tools

dastool
BSD

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

github.com/cmks/DAS_Tool 10.1038/s41564-018-0171-1
included in
mag
maintainers
Github user maxibor
Github user jfy133
get in touch
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