Description

Merge resolved cluster assemblies into final consensus outputs with Autocycler.

Input

name:type
description
pattern

meta{:bash}

:map

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

clusters{:bash}

:file

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

*.gfa

Output

name:type
description
pattern

fasta{:bash}

meta{:bash}

:map

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

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

:file

Consensus genome sequence generated by Autocycler.

combine/*/consensus_assembly.fasta

gfa{:bash}

meta{:bash}

:map

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

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

:file

Consensus assembly graph generated by Autocycler.

combine/*/consensus_assembly.gfa

stats{:bash}

meta{:bash}

:map

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

combine/${prefix}/consensus_assembly.yaml{:bash}

:file

Run statistics for the combine step.

combine/*/consensus_assembly.yaml

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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