subworkflows/fasta_newick_epang_gappa
Run phylogenetic placement with a number of query sequences plus a reference alignment and phylogeny. Used in nf-core/phyloplace.
phylogenetic placementphylogeneticsalignmentfastanewick
Description
Run phylogenetic placement with a number of query sequences plus a reference alignment and phylogeny. Used in nf-core/phyloplace.
Input
Name (Type)
Description
Pattern
Structure: [
meta: val(meta),
data: [
alignmethod: ‘hmmer’,
queryseqfile: path(“*.faa”),
refseqfile: path(“*.alnfaa”),
refphylogeny: path(“*.newick”),
model: “LG”,
taxonomy: path(“*.tsv”)
]
]
Fasta file with query sequences
*.{faa,fna,fa,fasta,fa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz} File with reference sequences; aligned unless an hmmfile is provided
*.{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} HMM file to use for alignment; implies that refseqfile is not aligned. Optional.
*.{hmm,HMM,hmm.gz,HMM.gz} included in
included modules and subworkflows
maintainer
