modules/cdhit_cdhit

Cluster protein sequences using sequence similarity

clusterproteinalignmentfasta

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

Description

Cluster protein sequences using sequence similarity

Input

name:type

description

pattern

`meta`
`:map`

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

`sequences`
`:file`

fasta file of sequences to be clustered

*.{fa,fasta}

Output

name:type

description

pattern

`fasta`

`meta`
`:map`

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

`*.fasta`
`:file`

fasta file of the representative sequences for each cluster

*.{fasta}

`clusters`

`meta`
`:map`

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

`*.clstr`
`:file`

List of clusters

*.{clstr}

`versions_cdhit`

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

The name of the process

`cdhit`
`:string`

The name of the tool

`cd-hit -h | sed -n '1s/.version $[0-9.]$.*/\1/p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`cdhit`
`:string`

The name of the tool

`cd-hit -h | sed -n '1s/.version $[0-9.]$.*/\1/p'`
`:eval`

The expression to obtain the version of the tool

Tools

cdhit
GPL v2

Clusters and compares protein or nucleotide sequences

sites.google.com/view/cd-hit/home github.com/weizhongli/cdhit/wiki https://github.com/weizhongli/cdhit 10.1093/bioinformatics/btl158

modules/cdhit_cdhit

Description

Input

`meta`
`:map`

`sequences`
`:file`

Output

`fasta`

`meta`
`:map`

`*.fasta`
`:file`

`clusters`

`meta`
`:map`

`*.clstr`
`:file`

`versions_cdhit`

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

`cdhit`
`:string`

`cd-hit -h | sed -n '1s/.version \([0-9.]\).*/\1/p'`
`:eval`

Topics

`versions`

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

`cdhit`
`:string`

`cd-hit -h | sed -n '1s/.version \([0-9.]\).*/\1/p'`
`:eval`

Tools

cdhit
GPL v2

included in

maintainers

get in touch

modules/cdhit_cdhit

Description

Input

meta:map

sequences:file

Output

fasta

meta:map

*.fasta:file

clusters

meta:map

*.clstr:file

versions_cdhit

${task.process}:string

cdhit:string

cd-hit -h | sed -n '1s/.*version \([0-9.]*\).*/\1/p':eval

Topics

versions

${task.process}:string

cdhit:string

cd-hit -h | sed -n '1s/.*version \([0-9.]*\).*/\1/p':eval

Tools

cdhit GPL v2

included in

maintainers

get in touch

`meta`
`:map`

`sequences`
`:file`

`fasta`

`meta`
`:map`

`*.fasta`
`:file`

`clusters`

`meta`
`:map`

`*.clstr`
`:file`

`versions_cdhit`

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

`cdhit`
`:string`

`cd-hit -h | sed -n '1s/.version \([0-9.]\).*/\1/p'`
`:eval`

`versions`

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

`cdhit`
`:string`

`cd-hit -h | sed -n '1s/.version \([0-9.]\).*/\1/p'`
`:eval`

cdhit
GPL v2