name: "fasta_newick_epang_gappa"
description: Run phylogenetic placement with a number of query sequences plus a reference alignment and phylogeny. Used in nf-core/phyloplace.
keywords:
  - phylogenetic placement
  - phylogenetics
  - alignment
  - fasta
  - newick
modules:
  - hmmer/hmmbuild
  - hmmer/hmmalign
  - hmmer/eslalimask
  - hmmer/eslreformat
  - mafft
  - epang/place
  - epang/split
  - gappa/examinegraft
  - gappa/examineassign
  - gappa/examineheattree
input:
  - ch_pp_data:
    type: map
    description: |
      Structure: [
        meta: val(meta),
        data: [
          alignmethod:  'hmmer',
          queryseqfile: path("*.faa"),
          refseqfile:   path("*.alnfaa"),
          refphylogeny: path("*.newick"),
          model:        "LG",
          taxonomy:     path("*.tsv")
        ]
      ]
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - queryseqfile:
      type: file
      description: Fasta file with query sequences
      pattern: "*.{faa,fna,fa,fasta,fa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz}"
  - refseqfile:
      type: file
      description: File with reference sequences; aligned unless an hmmfile is provided
      pattern: "*.{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}"
  - refphylogeny:
      type: file
      description: Newick file with reference phylogenetic tree
      pattern: "*.{newick,tree}"
  - hmmfile:
      type: file
      description: HMM file to use for alignment; implies that refseqfile is not aligned. Optional.
      pattern: "*.{hmm,HMM,hmm.gz,HMM.gz}"
  - model:
      type: string
      description: Phylogenetic model to use in placement, e.g. 'LG+F' or 'GTR+I+F'
  - alignmethod:
      type: string
      description: Method used for alignment, 'hmmer' or 'mafft'
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - epang:
      type: directory
      description: All output from EPA-NG
      pattern: "*"
  - jplace:
      type: file
      description: jplace file from EPA-NG
      pattern: "*.jplace"
  - grafted_phylogeny:
      type: file
      description: Newick file with query sequences placed in reference tree
      pattern: "*.newick"
  - taxonomy_profile:
      type: file
      description: Tab separated file with taxonomy information from classification
      pattern: "*.tsv"
  - taxonomy_per_query:
      type: file
      description: Tab separated file with taxonomy information per query from classification
      pattern: "*.tsv"
  - heattree:
      type: file
      description: Heattree in SVG format
      pattern: "*.svg"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@erikrikarddaniel"
