modules/autocycler_trim

Trim cluster assembly graphs to remove unsupported segments prior to resolution.

autocyclergenome-assemblygraph-trimminglong-read

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

Description

Trim cluster assembly graphs to remove unsupported segments prior to resolution.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`gfa`
`:file`

Cluster-specific assembly graph in GFA format.

*.gfa

Output

name:type

description

pattern

`gfa`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`trim/$prefix/*.gfa`
`:file`

Trimmed assembly graphs emitted by Autocycler.

trim/*/*.gfa

`stats`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`trim/$prefix/*.yaml`
`:file`

Trimming statistics for each cluster.

trim/*/*.yaml

`versions_autocycler`

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

The name of the process

`autocycler`
`:string`

The name of the tool

`autocycler --version | sed 's/^[^ ]* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`autocycler`
`:string`

The name of the tool

`autocycler --version | sed 's/^[^ ]* //'`
`:eval`

The expression to obtain the version of the tool

Tools

autocycler
GPL-3.0

A tools for generating consensus long-read assemblies for bacterial genomes.

github.com/rrwick/Autocycler/wiki https://github.com/rrwick/Autocycler 10.1093/bioinformatics/btaf474

modules/autocycler_trim

Description

Input

`meta`
`:map`

`gfa`
`:file`

Output

`gfa`

`meta`
`:map`

`trim/$prefix/*.gfa`
`:file`

`stats`

`meta`
`:map`

`trim/$prefix/*.yaml`
`:file`

`versions_autocycler`

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

`autocycler`
`:string`

`autocycler --version | sed 's/^[^ ]* //'`
`:eval`

Topics

`versions`

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

`autocycler`
`:string`

`autocycler --version | sed 's/^[^ ]* //'`
`:eval`

Tools

autocycler
GPL-3.0

maintainer

get in touch

modules/autocycler_trim

Description

Input

meta:map

gfa:file

Output

gfa

meta:map

trim/$prefix/*.gfa:file

stats

meta:map

trim/$prefix/*.yaml:file

versions_autocycler

${task.process}:string

autocycler:string

autocycler --version | sed 's/^[^ ]* //':eval

Topics

versions

${task.process}:string

autocycler:string

autocycler --version | sed 's/^[^ ]* //':eval

Tools

autocycler GPL-3.0

maintainer

get in touch

`meta`
`:map`

`gfa`
`:file`

`gfa`

`meta`
`:map`

`trim/$prefix/*.gfa`
`:file`

`stats`

`meta`
`:map`

`trim/$prefix/*.yaml`
`:file`

`versions_autocycler`

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

`autocycler`
`:string`

`autocycler --version | sed 's/^[^ ]* //'`
`:eval`

`versions`

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

`autocycler`
`:string`

`autocycler --version | sed 's/^[^ ]* //'`
`:eval`

autocycler
GPL-3.0