Phylo placement part 1

[erikrikarddaniel]

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