modules/concoct_mergecutupclustering

Merge consecutive parts of the original contigs original cut up by cut_up_fasta.py

contigsfragmentmagsbinningfastacutcut upmerge

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

Description

Merge consecutive parts of the original contigs original cut up by cut_up_fasta.py

Input

name:type

description

pattern

`meta`
`:map`

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

`clustering_csv`
`:file`

Input cutup clustering result. Typically *_gt1000.csv from concoct

*.csv

Output

name:type

description

pattern

`csv`

`meta`
`:map`

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

`*.csv`
`:file`

Cluster assignments per contig part with consensus cluster

*.csv

`versions_concoct`

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

The name of the process

`concoct`
`:string`

The name of the tool

`concoct --version | cut -d " " -f2`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`concoct`
`:string`

The name of the tool

`concoct --version | cut -d " " -f2`
`:eval`

The expression to obtain the version of the tool

Tools

concoct
FreeBSD

Clustering cONtigs with COverage and ComposiTion

concoct.readthedocs.io/en/latest https://github.com/BinPro/CONCOCT 10.1038/nmeth.3103

modules/concoct_mergecutupclustering

Description

Input

`meta`
`:map`

`clustering_csv`
`:file`

Output

`csv`

`meta`
`:map`

`*.csv`
`:file`

`versions_concoct`

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

`concoct`
`:string`

`concoct --version | cut -d " " -f2`
`:eval`

Topics

`versions`

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

`concoct`
`:string`

`concoct --version | cut -d " " -f2`
`:eval`

Tools

concoct
FreeBSD

included in

maintainer

get in touch

modules/concoct_mergecutupclustering

Description

Input

meta:map

clustering_csv:file

Output

csv

meta:map

*.csv:file

versions_concoct

${task.process}:string

concoct:string

concoct --version | cut -d " " -f2:eval

Topics

versions

${task.process}:string

concoct:string

concoct --version | cut -d " " -f2:eval

Tools

concoct FreeBSD

included in

maintainer

get in touch

`meta`
`:map`

`clustering_csv`
`:file`

`csv`

`meta`
`:map`

`*.csv`
`:file`

`versions_concoct`

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

`concoct`
`:string`

`concoct --version | cut -d " " -f2`
`:eval`

`versions`

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

`concoct`
`:string`

`concoct --version | cut -d " " -f2`
`:eval`

concoct
FreeBSD