Cluster replicons in compressed assemblies with Autocycler.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'sample1' ]
[ id:'sample1' ]
gfa{:bash}
:file
Assembly graph files produced by the compression step.
*/*.gfa
clusters{:bash}
clustering/$prefix/qc_pass/*/*.gfa{:bash}
Aassembly graphs of clustered contigs.
clustering/*/qc_pass/*/*.gfa
clusterstats{:bash}
clustering/$prefix/qc_pass/*/*.yaml{:bash}
Per-cluster metrics reported by Autocycler.
clustering/*/qc_pass/*/*.yaml
newick{:bash}
clustering/$prefix/*.newick{:bash}
Newick tree relating contigs.
clustering/*/*.newick
tsv{:bash}
clustering/$prefix/*.tsv{:bash}
Tabular summary of cluster relationships.
clustering/*/*.tsv
pairwisedistances{:bash}
clustering/$prefix/*.phylip{:bash}
Pairwise distance matrix in PHYLIP format.
clustering/*/*.phylip
stats{:bash}
clustering/$prefix/*.yaml{:bash}
Run-level statistics for the clustering step.
clustering/*/*.yaml
versions_autocycler{:bash}
${task.process}{:bash}
:string
The name of the process
autocycler{:bash}
The name of the tool
autocycler --version | sed 's/^[^ ]* //'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
A tools for generating consensus long-read assemblies for bacterial genomes.
