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

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/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.

Input

name

description

pattern

`ch_pp_data`

Phylogenetic placement input, one entry per sample, where:

alignmethod is the method used for alignment, ‘hmmer’, ‘clustalo’ or ‘mafft’
queryseqfile is a fasta file with query sequences
refseqfile is a file with reference sequences, aligned unless an hmmfile is provided
refphylogeny is a newick file with the reference phylogenetic tree
hmmfile is an optional HMM file to use for alignment; implies that refseqfile is not aligned
model is the phylogenetic model to use in placement, e.g. ‘LG+F’ or ‘GTR+I+F’
taxonomy is a tab separated file with taxonomy information for the reference sequences

Structure: [
meta: val(meta),
data: [
alignmethod: ‘hmmer’,
queryseqfile: path(“*.faa”),
refseqfile: path(“*.alnfaa”),
refphylogeny: path(“*.newick”),
hmmfile: path(“*.hmm”),
model: “LG”,
taxonomy: path(“*.tsv”)
]
]

`compress_alignment`

Write the clustalo and mafft profile alignments gzipped. Recommended for large
alignments, which are mostly gaps; hmmer alignments are not affected.

Output

name

description

pattern

`epang`

All output from EPA-NG.

Structure: [ val(meta), path(epang) ]

*

`jplace`

jplace file from EPA-NG.

Structure: [ val(meta), path(jplace) ]

*.jplace

`epang_log`

EPA-NG log file.

Structure: [ path(log) ]

*.epa_info.log

`grafted_phylogeny`

Newick file with query sequences placed in reference tree.

Structure: [ val(meta), path(newick) ]

*.newick

`taxonomy_profile`

Tab separated file with taxonomy information from classification.

Structure: [ val(meta), path(tsv) ]

*.tsv

`taxonomy_per_query`

Tab separated file with taxonomy information per query from classification.

Structure: [ val(meta), path(tsv) ]

*.tsv

`heattree`

Heattree in SVG format.

Structure: [ val(meta), path(svg) ]

*.svg

`hmmbuild_log`

hmmbuild output, for entries where the hmm was built from the reference alignment.

Structure: [ path(txt) ]

*.hmmbuild.txt