trees by Fred Lemoine : replace the code inside main.nf and debugged

This

    fasta=Reformat(aa_tsv_ch2)
    fastagroups=DefineGroups(fasta,parseDb_filtering.out.select_ch).flatten()
    align=Align(fastagroups,phylo_tree_heavy)
    // Keeps only alignments with at least 3 sequences
    filtered=NbSequences(align).filter{it[0].toInteger()>=3}.map{it->it[1]}
    tree=Tree(filtered,phylo_tree_model_file)
    itolmeta=ProcessMeta(meta_file)
    ITOL(tree[0],itolmeta,phylo_tree_itolkey)

has been removed from main.nf and must be replaced just before

    backup(
        config_file, 
        log_file
    )