modules/autocycler_resolve

Resolve trimmed assembly graphs into final contigs within Autocycler.

autocyclergenome-assemblygraph-resolutionlong-read

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

Description

Resolve trimmed assembly graphs into final contigs within Autocycler.

Input

name:type

description

pattern

`meta`
`:map`

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

`gfa`
`:file`

Trimmed assembly graph in GFA format from the previous step.

*.gfa

Output

name:type

description

pattern

`bridged`

`meta`
`:map`

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

`resolve/${prefix}/${prefix}_3_bridged.gfa`
`:file`

Assembly graph with bridges resolved.

resolve/*/*_3_bridged.gfa

`merged`

`meta`
`:map`

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

`resolve/${prefix}/${prefix}_4_merged.gfa`
`:file`

Merged assembly graph after bridging.

resolve/*/*_4_merged.gfa

`resolved`

`meta`
`:map`

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

`resolve/${prefix}/${prefix}_5_final.gfa`
`:file`

Final resolved assembly graph.

resolve/*/*_5_final.gfa

`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_resolve

Description

Input

`meta`
`:map`

`gfa`
`:file`

Output

`bridged`

`meta`
`:map`

`resolve/${prefix}/${prefix}_3_bridged.gfa`
`:file`

`merged`

`meta`
`:map`

`resolve/${prefix}/${prefix}_4_merged.gfa`
`:file`

`resolved`

`meta`
`:map`

`resolve/${prefix}/${prefix}_5_final.gfa`
`: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_resolve

Description

Input

meta:map

gfa:file

Output

bridged

meta:map

resolve/${prefix}/${prefix}_3_bridged.gfa:file

merged

meta:map

resolve/${prefix}/${prefix}_4_merged.gfa:file

resolved

meta:map

resolve/${prefix}/${prefix}_5_final.gfa: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`

`bridged`

`meta`
`:map`

`resolve/${prefix}/${prefix}_3_bridged.gfa`
`:file`

`merged`

`meta`
`:map`

`resolve/${prefix}/${prefix}_4_merged.gfa`
`:file`

`resolved`

`meta`
`:map`

`resolve/${prefix}/${prefix}_5_final.gfa`
`: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