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