Phylo placement part 1 - Githubissues

nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

https://nf-co.re/ampliseq

MIT License

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Phylo placement part 1 #561

Open erikrikarddaniel opened 1 year ago

erikrikarddaniel commented 1 year ago

Description of feature

Call the fasta_newick_epang_gappa subworkflow for all ASV sequence, given user specified parameters:

pplace_tree (A tree in newick format)
pplace_aln (The corresponding alignment in fasta format)
pplace_model (Phylogenetic model for the tree)
pplace_taxonomy (TSV file with sequence names (first column) and semicolon-separated taxonomy strings)
pplace_alnmethod (Alignment strategy to use; default hmmer)
pplace_name (Name to use for output files for this run, default user_tree)

Test data:

Ref. alignment: https://github.com/nf-core/test-datasets/raw/phyloplace/testdata/cyanos_16s.alnfna
Ref. tree: https://github.com/nf-core/test-datasets/raw/phyloplace/testdata/cyanos_16s.newick
Model: GTR+F+I+I+R3
Taxonomy: https://github.com/nf-core/test-datasets/raw/phyloplace/testdata/cyanos_16s.taxonomy.tsv