modules/binette

A fast and accurate binning refinement tool to construct high quality MAGs from the output of multiple binning tools.

binningrefinementgenomicsmetagenomicsmag

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

Description

A fast and accurate binning refinement tool to construct high quality MAGs from the output of multiple binning tools.

Input

name:type

description

pattern

`meta`
`:map`

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

`contig2bin`
`:file`

List of contig2bin files (headerless TSV with format contigname\tbinname)

*.tsv

`bindirs`
`:directory`

List of directories containing bin fasta files. All FASTA files should have the same extension.

`contigs`
`:file`

Fasta file containing contigs

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

`proteins`
`:file`

optional AA Fasta file containing contigs

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

`meta2`
`:map`

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

`checkm2_db`
`:file`

CheckM2 DIAMOND database file.

Output

name:type

description

pattern

`final_bins`

`meta`
`:map`

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

`final_bins/*.fa.gz`
`:file`

Refined bins in fasta format

*.fa.gz

`contig2bin`

`meta`
`:map`

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

`*.final_contig_to_bin.tsv`
`:file`

Final contig to bin assignment file

*.tsv

`input_bins_quality_reports`

`meta`
`:map`

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

`input_bins_quality_reports/*.tsv`
`:file`

Quality reports for input bins

*.tsv

`final_bins_quality_report`

`meta`
`:map`

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

`*.final_bins_quality_reports.tsv`
`:file`

Quality report for final refined bins

*.tsv

`versions_binette`

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

The name of the process

`binette`
`:string`

The name of the tool

`binette --version | sed 's/Binette //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`binette`
`:string`

The name of the tool

`binette --version | sed 's/Binette //'`
`:eval`

The expression to obtain the version of the tool

Tools

binette
GPL-3.0

Binette is a fast and accurate binning refinement tool designed to construct high-quality MAGs from the output of multiple binning tools.

binette.readthedocs.io https://github.com/genotoul-bioinfo/Binette

modules/binette

Description

Input

`meta`
`:map`

`contig2bin`
`:file`

`bindirs`
`:directory`

`contigs`
`:file`

`proteins`
`:file`

`meta2`
`:map`

`checkm2_db`
`:file`

Output

`final_bins`

`meta`
`:map`

`final_bins/*.fa.gz`
`:file`

`contig2bin`

`meta`
`:map`

`*.final_contig_to_bin.tsv`
`:file`

`input_bins_quality_reports`

`meta`
`:map`

`input_bins_quality_reports/*.tsv`
`:file`

`final_bins_quality_report`

`meta`
`:map`

`*.final_bins_quality_reports.tsv`
`:file`

`versions_binette`

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

`binette`
`:string`

`binette --version | sed 's/Binette //'`
`:eval`

Topics

`versions`

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

`binette`
`:string`

`binette --version | sed 's/Binette //'`
`:eval`

Tools

binette
GPL-3.0

maintainer

get in touch

modules/binette

Description

Input

meta :map

contig2bin :file

bindirs :directory

contigs :file

proteins :file

meta2 :map

checkm2_db :file

Output

final_bins

meta :map

final_bins/*.fa.gz :file

contig2bin

meta :map

*.final_contig_to_bin.tsv :file

input_bins_quality_reports

meta :map

input_bins_quality_reports/*.tsv :file

final_bins_quality_report

meta :map

*.final_bins_quality_reports.tsv :file

versions_binette

${task.process} :string

binette :string

binette --version | sed 's/Binette //' :eval

Topics

versions

${task.process} :string

binette :string

binette --version | sed 's/Binette //' :eval

Tools

binetteGPL-3.0

maintainer

get in touch

`meta`
`:map`

`contig2bin`
`:file`

`bindirs`
`:directory`

`contigs`
`:file`

`proteins`
`:file`

`meta2`
`:map`

`checkm2_db`
`:file`

`final_bins`

`meta`
`:map`

`final_bins/*.fa.gz`
`:file`

`contig2bin`

`meta`
`:map`

`*.final_contig_to_bin.tsv`
`:file`

`input_bins_quality_reports`

`meta`
`:map`

`input_bins_quality_reports/*.tsv`
`:file`

`final_bins_quality_report`

`meta`
`:map`

`*.final_bins_quality_reports.tsv`
`:file`

`versions_binette`

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

`binette`
`:string`

`binette --version | sed 's/Binette //'`
`:eval`

`versions`

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

`binette`
`:string`

`binette --version | sed 's/Binette //'`
`:eval`

binette
GPL-3.0