Description

Resolve trimmed assembly graphs into final contigs within Autocycler.

Input

name:type
description
pattern

meta{:bash}

:map

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

gfa{:bash}

:file

Trimmed assembly graph in GFA format from the previous step.

*.gfa

Output

name:type
description
pattern

bridged{:bash}

meta{:bash}

:map

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

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

:file

Assembly graph with bridges resolved.

resolve/*/*_3_bridged.gfa

merged{:bash}

meta{:bash}

:map

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

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

:file

Merged assembly graph after bridging.

resolve/*/*_4_merged.gfa

resolved{:bash}

meta{:bash}

:map

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

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

:file

Final resolved assembly graph.

resolve/*/*_5_final.gfa

versions_autocycler{:bash}

${task.process}{:bash}

:string

The name of the process

autocycler{:bash}

:string

The name of the tool

autocycler --version | sed 's/^[^ ]* //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

autocycler{:bash}

:string

The name of the tool

autocycler --version | sed 's/^[^ ]* //'{:bash}

: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
maintainer
Github user dwells-eit
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