kkonganti@11: params {
kkonganti@11:     workflow_conceived_by = 'Kranti Konganti'
kkonganti@11:     workflow_built_by = 'Kranti Konganti'
kkonganti@11:     workflow_version = '0.2.0'
kkonganti@11:     ref_acc =  'GCF_003516125'
kkonganti@11:     cronology_root_dbdir = '/galaxy/cfsan-centriflaken-db/cronology/PDG000000043.213'
kkonganti@11:     upload_microreact = true
kkonganti@11:     microreact_api_key = ("${projectDir}"
kkonganti@11:         + File.separator
kkonganti@11:         + 'assets'
kkonganti@11:         + File.separator
kkonganti@11:         + 'microreact_api.key')
kkonganti@11:     microreact_tree_name = 'cronology_run_tree'
kkonganti@11:     dpubmlstpy_run = true
kkonganti@11:     dpubmlstpy_org = 'cronobacter'
kkonganti@11:     dpubmlstpy_mlsts = 'schemes/1'
kkonganti@11:     dpubmlstpy_profile = false
kkonganti@11:     dpubmlstpy_loci = false
kkonganti@11:     dpubmlstpy_suffix = false
kkonganti@11:     dpubmlstpy_akey = false
kkonganti@11:     dpubmlstpy_id = false
kkonganti@11:     fastp_run = true
kkonganti@11:     fastp_failed_out = false
kkonganti@11:     fastp_merged_out = false
kkonganti@11:     fastp_overlapped_out = false
kkonganti@11:     fastp_6 = false
kkonganti@11:     fastp_reads_to_process = 0 
kkonganti@11:     fastp_fix_mgi_id = false
kkonganti@11:     fastp_A = false
kkonganti@11:     fastp_f = 0
kkonganti@11:     fastp_t = 0
kkonganti@11:     fastp_b = 0
kkonganti@11:     fastp_F = 0
kkonganti@11:     fastp_T = 0
kkonganti@11:     fastp_B = 0
kkonganti@11:     fastp_dedup = true
kkonganti@11:     fastp_dup_calc_accuracy = 6
kkonganti@11:     fastp_poly_g_min_len = 10
kkonganti@11:     fastp_G = true
kkonganti@11:     fastp_x = false
kkonganti@11:     fastp_poly_x_min_len = 10 
kkonganti@11:     fastp_cut_front = true
kkonganti@11:     fastp_cut_tail = false
kkonganti@11:     fastp_cut_right = true
kkonganti@11:     fastp_W = 20
kkonganti@11:     fastp_M = 30
kkonganti@11:     fastp_q = 30
kkonganti@11:     fastp_u = 40
kkonganti@11:     fastp_n = 5
kkonganti@11:     fastp_e = 0
kkonganti@11:     fastp_l = 35
kkonganti@11:     fastp_max_len = 0
kkonganti@11:     fastp_y = true
kkonganti@11:     fastp_Y = 30
kkonganti@11:     fastp_U = false
kkonganti@11:     fastp_umi_loc = false
kkonganti@11:     fastp_umi_len = false
kkonganti@11:     fastp_umi_prefix = false
kkonganti@11:     fastp_umi_skip = false
kkonganti@11:     fastp_p = true
kkonganti@11:     fastp_P = 20
kkonganti@11:     fastp_use_custom_adapters = false
kkonganti@11:     fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
kkonganti@11:         + File.separator
kkonganti@11:         + 'assets'
kkonganti@11:         + File.separator
kkonganti@11:         + 'adaptors.fa' : false)
kkonganti@11:     mashscreen_w = false
kkonganti@11:     mashscreen_i = false
kkonganti@11:     mashscreen_v = false
kkonganti@11:     tuspy_run = true
kkonganti@11:     tuspy_s = false
kkonganti@11:     tuspy_m = false
kkonganti@11:     tuspy_ps = (params.cronology_root_dbdir
kkonganti@11:         + File.separator
kkonganti@11:         + 'index_pdg_metadata' 
kkonganti@11:         + File.separator
kkonganti@11:         + 'IDXD_PDG_METAD.pickle')
kkonganti@11:     tuspy_gd = (params.cronology_root_dbdir 
kkonganti@11:         + File.separator 
kkonganti@11:         + 'scaffold_genomes')
kkonganti@11:     tuspy_gds = '_scaffolded_genomic.fna.gz'
kkonganti@11:     tuspy_n = 5
kkonganti@11:     spades_run = false
kkonganti@11:     spades_isolate = false
kkonganti@11:     spades_sc = false
kkonganti@11:     spades_meta = true
kkonganti@11:     spades_bio = false
kkonganti@11:     spades_corona = false
kkonganti@11:     spades_rna = false
kkonganti@11:     spades_plasmid = false
kkonganti@11:     spades_metaviral = false
kkonganti@11:     spades_metaplasmid = false
kkonganti@11:     spades_rnaviral = false
kkonganti@11:     spades_iontorrent = false
kkonganti@11:     spades_only_assembler = false
kkonganti@11:     spades_careful = false
kkonganti@11:     spades_cov_cutoff = false
kkonganti@11:     spades_k = false
kkonganti@11:     spades_hmm = false
kkonganti@11:     shovill_run = true
kkonganti@11:     shovill_depth = 150
kkonganti@11:     shovill_gsize = false
kkonganti@11:     shovill_minlen = 200
kkonganti@11:     shovill_mincov = 5
kkonganti@11:     shovill_namefmt = false
kkonganti@11:     shovill_keepfiles = false
kkonganti@11:     shovill_assembler = false
kkonganti@11:     shovill_opts = false
kkonganti@11:     shovill_kmers = false
kkonganti@11:     shovill_trim = false
kkonganti@11:     shovill_noreadcorr = false
kkonganti@11:     shovill_nostitch = false
kkonganti@11:     shovill_nocorr = false
kkonganti@11:     polypolish_run = true
kkonganti@11:     polypolish_d = 5
kkonganti@11:     polypolish_i = 0.2
kkonganti@11:     polypolish_m = 10
kkonganti@11:     polypolish_v = 0.5
kkonganti@11:     mashtree_run = true
kkonganti@11:     mashtree_fofn = true
kkonganti@11:     mashtree_trunclength = false
kkonganti@11:     mashtree_mindepth = false
kkonganti@11:     mashtree_kmerlength = false
kkonganti@11:     mashtree_sketchsize = false 
kkonganti@11:     mashtree_seed = false
kkonganti@11:     mashtree_genomesize = false
kkonganti@11:     mashtree_sigfigs = false
kkonganti@11:     mashtree_sortorder = false
kkonganti@11:     quast_run = true
kkonganti@11:     quast_min_contig = 200
kkonganti@11:     quast_split_scaffolds = false
kkonganti@11:     quast_euk = false
kkonganti@11:     quast_fungal = false
kkonganti@11:     quast_large = false
kkonganti@11:     quast_k = false
kkonganti@11:     quast_kmer_size = false 
kkonganti@11:     quast_circos = true
kkonganti@11:     quast_glimmer = true
kkonganti@11:     quast_gene_thr = '0,300,1500,3000'
kkonganti@11:     quast_rna_finding = true
kkonganti@11:     quast_ref_size = false
kkonganti@11:     quast_ctg_thr = '0,1000,5000,10000,25000,50000'
kkonganti@11:     quast_x_for_nx = 90
kkonganti@11:     quast_use_all_alns = false
kkonganti@11:     quast_min_alignment = 65
kkonganti@11:     quast_min_identity = '95.0'
kkonganti@11:     quast_ambig_usage = 'one'
kkonganti@11:     quast_ambig_score = '0.99'
kkonganti@11:     quast_strict_na = false
kkonganti@11:     quast_x = 1000
kkonganti@11:     quast_local_mis_size = 200 
kkonganti@11:     quast_sca_gap_size = 10000
kkonganti@11:     quast_unaln_part_size = 500
kkonganti@11:     quast_skip_unaln_mis_ctgs = false
kkonganti@11:     quast_fragmented = false
kkonganti@11:     quast_frag_max_ident = (params.quast_fragmented ? 200 : false)
kkonganti@11:     quast_plots_format = 'pdf'
kkonganti@11:     prodka_run = true
kkonganti@11:     prodigal_run = (params.prodka_run ?: false)
kkonganti@11:     prodigal_c = false
kkonganti@11:     prodigal_f = 'gbk'
kkonganti@11:     prodigal_g = 11
kkonganti@11:     prodigal_m = true
kkonganti@11:     prodigal_n = false
kkonganti@11:     prodigal_p = 'single'
kkonganti@11:     prodigal_t = true
kkonganti@11:     prokka_run = (params.prodka_run ?: false)
kkonganti@11:     prokka_dbdir = false
kkonganti@11:     prokka_addgenes = true
kkonganti@11:     prokka_addmrna = true
kkonganti@11:     prokka_locustag = false
kkonganti@11:     prokka_increment = false
kkonganti@11:     prokka_gffver = false
kkonganti@11:     prokka_compliant = true
kkonganti@11:     prokka_centre = 'CFSAN-FDA'
kkonganti@11:     prokka_accver = false
kkonganti@11:     prokka_genus = (params.dpubmlstpy_org.capitalize() ?: 'Cronobacter')
kkonganti@11:     prokka_species = false
kkonganti@11:     prokka_strain = false
kkonganti@11:     prokka_plasmid = false
kkonganti@11:     prokka_kingdom = false
kkonganti@11:     prokka_gcode = false
kkonganti@11:     prokka_usegenus = true
kkonganti@11:     prokka_metagenome = false
kkonganti@11:     prokka_rawproduct = false
kkonganti@11:     prokka_cdsrnaolap = false
kkonganti@11:     prokka_evalue = '1e-9'
kkonganti@11:     prokka_coverage = 80
kkonganti@11:     prokka_fast = false
kkonganti@11:     prokka_noanno = false
kkonganti@11:     prokka_mincontiglen = 200 
kkonganti@11:     prokka_rfam = false
kkonganti@11:     prokka_norrna = false
kkonganti@11:     prokka_notrna = false
kkonganti@11:     prokka_rnammer = false
kkonganti@11:     pirate_run = false
kkonganti@11:     pirate_steps = false
kkonganti@11:     pirate_features = false 
kkonganti@11:     pirate_nucl = false
kkonganti@11:     pirate_pan_opt = "'--diamond'"
kkonganti@11:     pirate_pan_off = false
kkonganti@11:     pirate_min_len = 200
kkonganti@11:     pirate_para_off = false
kkonganti@11:     pirate_para_args = false
kkonganti@11:     pirate_classify_off = false
kkonganti@11:     pirate_align = false
kkonganti@11:     pirate_rplots = false
kkonganti@11:     mashscreen_run = true
kkonganti@11:     mash_sketch = (params.cronology_root_dbdir
kkonganti@11:         + File.separator 
kkonganti@11:         + 'mash_paste' 
kkonganti@11:         + File.separator 
kkonganti@11:         + 'msh.k21.1000h.' 
kkonganti@11:         + getPDGRelease(params.cronology_root_dbdir)
kkonganti@11:         + '.msh')
kkonganti@11:     mlst_run = true
kkonganti@11:     mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
kkonganti@11:     mlst_legacy = true
kkonganti@11:     mlst_minid = 95
kkonganti@11:     mlst_mincov = 10
kkonganti@11:     mlst_minscore = 50
kkonganti@11:     mlst_blastdb = false
kkonganti@11:     mlst_datadir = false
kkonganti@11:     mlst_label = true
kkonganti@11:     abricate_run = true
kkonganti@11:     abricate_datadir = ("${projectDir}"
kkonganti@11:         + File.separator
kkonganti@11:         + 'assets'
kkonganti@11:         + File.separator
kkonganti@11:         + 'abricate_dbs')
kkonganti@11:     abricate_minid = 90
kkonganti@11:     abricate_mincov = 80
kkonganti@11:     abricate_summary_run = true
kkonganti@11:     fq_filter_by_len = 0
kkonganti@11:     fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
kkonganti@11:     fq2_suffix = '_R2_001.fastq.gz'
kkonganti@11: }
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */
kkonganti@11: 
kkonganti@11: def getPDGRelease(db_path) {
kkonganti@11: 	db_path_obj = new File( db_path )
kkonganti@11: 	def pdg_release = []
kkonganti@11: 
kkonganti@11: 	db_path_obj.eachDirRecurse {
kkonganti@11: 		it.toString() =~ /PDG/ \
kkonganti@11:             ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
kkonganti@11:             : null
kkonganti@11: 	}
kkonganti@11: 
kkonganti@11: 	return pdg_release.unique().join('').toString()
kkonganti@11: }