splits an alignment into reference and query parts
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
refaln{:bash}
:file
reference alignment in any supported format including phylip and fasta, may be gzipped
*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}
fullaln{:bash}
full alignment in any supported format to split into reference and query alignments
query{:bash}
*query.fasta.gz{:bash}
query sequence alignment in gzipped fasta format
reference{:bash}
*reference.fasta.gz{:bash}
reference sequence alignment in gzipped fasta format
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Massively parallel phylogenetic placement of genetic sequences
