modules/autocycler_combine

Merge resolved cluster assemblies into final consensus outputs with Autocycler.

autocyclergenome-assemblyconsensuslong-read

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

Description

Merge resolved cluster assemblies into final consensus outputs with Autocycler.

Input

name:type

description

pattern

`meta`
`:map`

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

`clusters`
`:file`

Final cluster assembly graphs (GFA) to be combined into consensus sequences.

*.gfa

Output

name:type

description

pattern

`fasta`

`meta`
`:map`

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

`combine/${prefix}/consensus_assembly.fasta`
`:file`

Consensus genome sequence generated by Autocycler.

combine/*/consensus_assembly.fasta

`gfa`

`meta`
`:map`

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

`combine/${prefix}/consensus_assembly.gfa`
`:file`

Consensus assembly graph generated by Autocycler.

combine/*/consensus_assembly.gfa

`stats`

`meta`
`:map`

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

`combine/${prefix}/consensus_assembly.yaml`
`:file`

Run statistics for the combine step.

combine/*/consensus_assembly.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_combine

Description

Input

`meta`
`:map`

`clusters`
`:file`

Output

`fasta`

`meta`
`:map`

`combine/${prefix}/consensus_assembly.fasta`
`:file`

`gfa`

`meta`
`:map`

`combine/${prefix}/consensus_assembly.gfa`
`:file`

`stats`

`meta`
`:map`

`combine/${prefix}/consensus_assembly.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_combine

Description

Input

meta:map

clusters:file

Output

fasta

meta:map

combine/${prefix}/consensus_assembly.fasta:file

gfa

meta:map

combine/${prefix}/consensus_assembly.gfa:file

stats

meta:map

combine/${prefix}/consensus_assembly.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`

`clusters`
`:file`

`fasta`

`meta`
`:map`

`combine/${prefix}/consensus_assembly.fasta`
`:file`

`gfa`

`meta`
`:map`

`combine/${prefix}/consensus_assembly.gfa`
`:file`

`stats`

`meta`
`:map`

`combine/${prefix}/consensus_assembly.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