--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/workflows/conf/cronology.config	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,250 @@
+params {
+    workflow_conceived_by = 'Kranti Konganti'
+    workflow_built_by = 'Kranti Konganti'
+    workflow_version = '0.1.0'
+    ref_acc =  'GCF_003516125'
+    cronology_root_dbdir = '/hpc/scratch/Kranti.Konganti/trash/cronobacter/test_nf_db'
+    dpubmlstpy_run = true
+    dpubmlstpy_org = 'cronobacter'
+    dpubmlstpy_mlsts = 'schemes/1'
+    dpubmlstpy_profile = false
+    dpubmlstpy_loci = false
+    dpubmlstpy_suffix = false
+    dpubmlstpy_akey = false
+    dpubmlstpy_id = false
+    fastp_run = true
+    fastp_failed_out = false
+    fastp_merged_out = false
+    fastp_overlapped_out = false
+    fastp_6 = false
+    fastp_reads_to_process = 0 
+    fastp_fix_mgi_id = false
+    fastp_A = false
+    fastp_f = 0
+    fastp_t = 0
+    fastp_b = 0
+    fastp_F = 0
+    fastp_T = 0
+    fastp_B = 0
+    fastp_dedup = true
+    fastp_dup_calc_accuracy = 6
+    fastp_poly_g_min_len = 10
+    fastp_G = true
+    fastp_x = false
+    fastp_poly_x_min_len = 10 
+    fastp_cut_front = true
+    fastp_cut_tail = false
+    fastp_cut_right = true
+    fastp_W = 20
+    fastp_M = 30
+    fastp_q = 30
+    fastp_u = 40
+    fastp_n = 5
+    fastp_e = 0
+    fastp_l = 35
+    fastp_max_len = 0
+    fastp_y = true
+    fastp_Y = 30
+    fastp_U = false
+    fastp_umi_loc = false
+    fastp_umi_len = false
+    fastp_umi_prefix = false
+    fastp_umi_skip = false
+    fastp_p = true
+    fastp_P = 20
+    fastp_use_custom_adapters = false
+    fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
+        + File.separator
+        + 'assets'
+        + File.separator
+        + 'adaptors.fa' : false)
+    mashscreen_w = false
+    mashscreen_i = false
+    mashscreen_v = false
+    tuspy_run = true
+    tuspy_s = false
+    tuspy_m = false
+    tuspy_ps = (params.cronology_root_dbdir
+        + File.separator
+        + 'index_pdg_metadata' 
+        + File.separator
+        + 'IDXD_PDG_METAD.pickle')
+    tuspy_gd = (params.cronology_root_dbdir 
+        + File.separator 
+        + 'scaffold_genomes')
+    tuspy_gds = '_scaffolded_genomic.fna.gz'
+    tuspy_n = 5
+    spades_run = false
+    spades_isolate = false
+    spades_sc = false
+    spades_meta = true
+    spades_bio = false
+    spades_corona = false
+    spades_rna = false
+    spades_plasmid = false
+    spades_metaviral = false
+    spades_metaplasmid = false
+    spades_rnaviral = false
+    spades_iontorrent = false
+    spades_only_assembler = false
+    spades_careful = false
+    spades_cov_cutoff = false
+    spades_k = false
+    spades_hmm = false
+    shovill_run = true
+    shovill_depth = 150
+    shovill_gsize = false
+    shovill_minlen = 200
+    shovill_mincov = 5
+    shovill_namefmt = false
+    shovill_keepfiles = false
+    shovill_assembler = false
+    shovill_opts = false
+    shovill_kmers = false
+    shovill_trim = false
+    shovill_noreadcorr = false
+    shovill_nostitch = false
+    shovill_nocorr = false
+    polypolish_run = true
+    polypolish_d = 5
+    polypolish_i = 0.2
+    polypolish_m = 10
+    polypolish_v = 0.5
+    mashtree_run = true
+    mashtree_fofn = true
+    mashtree_trunclength = false
+    mashtree_mindepth = false
+    mashtree_kmerlength = false
+    mashtree_sketchsize = false 
+    mashtree_seed = false
+    mashtree_genomesize = false
+    mashtree_sigfigs = false
+    mashtree_sortorder = false
+    quast_run = true
+    quast_min_contig = 200
+    quast_split_scaffolds = false
+    quast_euk = false
+    quast_fungal = false
+    quast_large = false
+    quast_k = false
+    quast_kmer_size = false 
+    quast_circos = true
+    quast_glimmer = true
+    quast_gene_thr = '0,300,1500,3000'
+    quast_rna_finding = true
+    quast_ref_size = false
+    quast_ctg_thr = '0,1000,5000,10000,25000,50000'
+    quast_x_for_nx = 90
+    quast_use_all_alns = false
+    quast_min_alignment = 65
+    quast_min_identity = '95.0'
+    quast_ambig_usage = 'one'
+    quast_ambig_score = '0.99'
+    quast_strict_na = false
+    quast_x = 1000
+    quast_local_mis_size = 200 
+    quast_sca_gap_size = 10000
+    quast_unaln_part_size = 500
+    quast_skip_unaln_mis_ctgs = false
+    quast_fragmented = false
+    quast_frag_max_ident = (params.quast_fragmented ? 200 : false)
+    quast_plots_format = 'pdf'
+    prodka_run = true
+    prodigal_run = (params.prodka_run ?: false)
+    prodigal_c = false
+    prodigal_f = 'gbk'
+    prodigal_g = 11
+    prodigal_m = true
+    prodigal_n = false
+    prodigal_p = 'single'
+    prodigal_t = true
+    prokka_run = (params.prodka_run ?: false)
+    prokka_dbdir = false
+    prokka_addgenes = true
+    prokka_addmrna = true
+    prokka_locustag = false
+    prokka_increment = false
+    prokka_gffver = false
+    prokka_compliant = true
+    prokka_centre = 'CFSAN-FDA'
+    prokka_accver = false
+    prokka_genus = (params.dpubmlstpy_org.capitalize() ?: 'Cronobacter')
+    prokka_species = false
+    prokka_strain = false
+    prokka_plasmid = false
+    prokka_kingdom = false
+    prokka_gcode = false
+    prokka_usegenus = true
+    prokka_metagenome = false
+    prokka_rawproduct = false
+    prokka_cdsrnaolap = false
+    prokka_evalue = '1e-9'
+    prokka_coverage = 80
+    prokka_fast = false
+    prokka_noanno = false
+    prokka_mincontiglen = 200 
+    prokka_rfam = false
+    prokka_norrna = false
+    prokka_notrna = false
+    prokka_rnammer = false
+    pirate_run = false
+    pirate_steps = false
+    pirate_features = false 
+    pirate_nucl = false
+    pirate_pan_opt = "'--diamond'"
+    pirate_pan_off = false
+    pirate_min_len = 200
+    pirate_para_off = false
+    pirate_para_args = false
+    pirate_classify_off = false
+    pirate_align = false
+    pirate_rplots = false
+    mashscreen_run = true
+    mash_sketch = (params.cronology_root_dbdir
+        + File.separator 
+        + 'mash_paste' 
+        + File.separator 
+        + 'msh.k21.1000h.' 
+        + getPDGRelease(params.cronology_root_dbdir)
+        + '.msh')
+    mlst_run = true
+    mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
+    mlst_legacy = true
+    mlst_minid = 95
+    mlst_mincov = 10
+    mlst_minscore = 50
+    mlst_blastdb = false
+    mlst_datadir = false
+    mlst_label = true
+    abricate_run = true
+    abricate_datadir = ("${projectDir}"
+        + File.separator
+        + 'assets'
+        + File.separator
+        + 'abricate_dbs')
+    abricate_minid = 90
+    abricate_mincov = 80
+    abricate_summary_run = true
+    fq_filter_by_len = 0
+    fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
+    fq2_suffix = '_R2_001.fastq.gz'
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+def getPDGRelease(db_path) {
+	db_path_obj = new File( db_path )
+	def pdg_release = []
+
+	db_path_obj.eachDirRecurse {
+		it.toString() =~ /PDG/ \
+            ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
+            : null
+	}
+
+	return pdg_release.unique().join('').toString()
+}