Predict recomination events in bacterial genomes
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
newick
:file
A Newick formatted tree based on multiple sequence alignment
*.{newick,treefile,dnd}
msa
A multiple sequence alignment in FASTA format
*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}
emsim
*.emsim.txt
Bootstrapped values for the three parameters R/theta, nu and delta
em
*.em.txt
Point estimates for R/theta, nu, delta and the branch lengths
status
*.importation_status.txt
List of reconstructed recombination events
*.labelled_tree.newick
Tree with all nodes labelled
fasta
*.ML_sequence.fasta
Sequence reconstructed by maximum likelihood
pos_ref
*.position_cross_reference.txt
CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta
versions_clonalframeml
${task.process}
:string
The name of the process
clonalframeml
The name of the tool
ClonalFrameML -version 2>&1 | sed 's/^.*ClonalFrameML v//'
:eval
The expression to obtain the version of the tool
versions
Efficient inferencing of recombination in bacterial genomes
