Mercurial > repos > kkonganti > cfsan_cronology

annotate 0.1.0/workflows/conf/cronology.config @ 6:a3c1cba6f773

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 19:52:20 -0500
parents 7ac696717239
children
rev   line source
kkonganti@0 1 params {
kkonganti@0 2 workflow_conceived_by = 'Kranti Konganti'
kkonganti@0 3 workflow_built_by = 'Kranti Konganti'
kkonganti@0 4 workflow_version = '0.1.0'
kkonganti@0 5 ref_acc = 'GCF_003516125'
kkonganti@4 6 cronology_root_dbdir = '/tool/tool-data/cfsan_cronology_db/0.1.0'
kkonganti@0 7 dpubmlstpy_run = true
kkonganti@0 8 dpubmlstpy_org = 'cronobacter'
kkonganti@0 9 dpubmlstpy_mlsts = 'schemes/1'
kkonganti@0 10 dpubmlstpy_profile = false
kkonganti@0 11 dpubmlstpy_loci = false
kkonganti@0 12 dpubmlstpy_suffix = false
kkonganti@0 13 dpubmlstpy_akey = false
kkonganti@0 14 dpubmlstpy_id = false
kkonganti@0 15 fastp_run = true
kkonganti@0 16 fastp_failed_out = false
kkonganti@0 17 fastp_merged_out = false
kkonganti@0 18 fastp_overlapped_out = false
kkonganti@0 19 fastp_6 = false
kkonganti@0 20 fastp_reads_to_process = 0
kkonganti@0 21 fastp_fix_mgi_id = false
kkonganti@0 22 fastp_A = false
kkonganti@0 23 fastp_f = 0
kkonganti@0 24 fastp_t = 0
kkonganti@0 25 fastp_b = 0
kkonganti@0 26 fastp_F = 0
kkonganti@0 27 fastp_T = 0
kkonganti@0 28 fastp_B = 0
kkonganti@0 29 fastp_dedup = true
kkonganti@0 30 fastp_dup_calc_accuracy = 6
kkonganti@0 31 fastp_poly_g_min_len = 10
kkonganti@0 32 fastp_G = true
kkonganti@0 33 fastp_x = false
kkonganti@0 34 fastp_poly_x_min_len = 10
kkonganti@0 35 fastp_cut_front = true
kkonganti@0 36 fastp_cut_tail = false
kkonganti@0 37 fastp_cut_right = true
kkonganti@0 38 fastp_W = 20
kkonganti@0 39 fastp_M = 30
kkonganti@0 40 fastp_q = 30
kkonganti@0 41 fastp_u = 40
kkonganti@0 42 fastp_n = 5
kkonganti@0 43 fastp_e = 0
kkonganti@0 44 fastp_l = 35
kkonganti@0 45 fastp_max_len = 0
kkonganti@0 46 fastp_y = true
kkonganti@0 47 fastp_Y = 30
kkonganti@0 48 fastp_U = false
kkonganti@0 49 fastp_umi_loc = false
kkonganti@0 50 fastp_umi_len = false
kkonganti@0 51 fastp_umi_prefix = false
kkonganti@0 52 fastp_umi_skip = false
kkonganti@0 53 fastp_p = true
kkonganti@0 54 fastp_P = 20
kkonganti@0 55 fastp_use_custom_adapters = false
kkonganti@0 56 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
kkonganti@0 57 + File.separator
kkonganti@0 58 + 'assets'
kkonganti@0 59 + File.separator
kkonganti@0 60 + 'adaptors.fa' : false)
kkonganti@0 61 mashscreen_w = false
kkonganti@0 62 mashscreen_i = false
kkonganti@0 63 mashscreen_v = false
kkonganti@0 64 tuspy_run = true
kkonganti@0 65 tuspy_s = false
kkonganti@0 66 tuspy_m = false
kkonganti@0 67 tuspy_ps = (params.cronology_root_dbdir
kkonganti@0 68 + File.separator
kkonganti@0 69 + 'index_pdg_metadata'
kkonganti@0 70 + File.separator
kkonganti@0 71 + 'IDXD_PDG_METAD.pickle')
kkonganti@0 72 tuspy_gd = (params.cronology_root_dbdir
kkonganti@0 73 + File.separator
kkonganti@0 74 + 'scaffold_genomes')
kkonganti@0 75 tuspy_gds = '_scaffolded_genomic.fna.gz'
kkonganti@0 76 tuspy_n = 5
kkonganti@0 77 spades_run = false
kkonganti@0 78 spades_isolate = false
kkonganti@0 79 spades_sc = false
kkonganti@0 80 spades_meta = true
kkonganti@0 81 spades_bio = false
kkonganti@0 82 spades_corona = false
kkonganti@0 83 spades_rna = false
kkonganti@0 84 spades_plasmid = false
kkonganti@0 85 spades_metaviral = false
kkonganti@0 86 spades_metaplasmid = false
kkonganti@0 87 spades_rnaviral = false
kkonganti@0 88 spades_iontorrent = false
kkonganti@0 89 spades_only_assembler = false
kkonganti@0 90 spades_careful = false
kkonganti@0 91 spades_cov_cutoff = false
kkonganti@0 92 spades_k = false
kkonganti@0 93 spades_hmm = false
kkonganti@0 94 shovill_run = true
kkonganti@0 95 shovill_depth = 150
kkonganti@0 96 shovill_gsize = false
kkonganti@0 97 shovill_minlen = 200
kkonganti@0 98 shovill_mincov = 5
kkonganti@0 99 shovill_namefmt = false
kkonganti@0 100 shovill_keepfiles = false
kkonganti@0 101 shovill_assembler = false
kkonganti@0 102 shovill_opts = false
kkonganti@0 103 shovill_kmers = false
kkonganti@0 104 shovill_trim = false
kkonganti@0 105 shovill_noreadcorr = false
kkonganti@0 106 shovill_nostitch = false
kkonganti@0 107 shovill_nocorr = false
kkonganti@0 108 polypolish_run = true
kkonganti@0 109 polypolish_d = 5
kkonganti@0 110 polypolish_i = 0.2
kkonganti@0 111 polypolish_m = 10
kkonganti@0 112 polypolish_v = 0.5
kkonganti@0 113 mashtree_run = true
kkonganti@0 114 mashtree_fofn = true
kkonganti@0 115 mashtree_trunclength = false
kkonganti@0 116 mashtree_mindepth = false
kkonganti@0 117 mashtree_kmerlength = false
kkonganti@0 118 mashtree_sketchsize = false
kkonganti@0 119 mashtree_seed = false
kkonganti@0 120 mashtree_genomesize = false
kkonganti@0 121 mashtree_sigfigs = false
kkonganti@0 122 mashtree_sortorder = false
kkonganti@0 123 quast_run = true
kkonganti@0 124 quast_min_contig = 200
kkonganti@0 125 quast_split_scaffolds = false
kkonganti@0 126 quast_euk = false
kkonganti@0 127 quast_fungal = false
kkonganti@0 128 quast_large = false
kkonganti@0 129 quast_k = false
kkonganti@0 130 quast_kmer_size = false
kkonganti@0 131 quast_circos = true
kkonganti@0 132 quast_glimmer = true
kkonganti@0 133 quast_gene_thr = '0,300,1500,3000'
kkonganti@0 134 quast_rna_finding = true
kkonganti@0 135 quast_ref_size = false
kkonganti@0 136 quast_ctg_thr = '0,1000,5000,10000,25000,50000'
kkonganti@0 137 quast_x_for_nx = 90
kkonganti@0 138 quast_use_all_alns = false
kkonganti@0 139 quast_min_alignment = 65
kkonganti@0 140 quast_min_identity = '95.0'
kkonganti@0 141 quast_ambig_usage = 'one'
kkonganti@0 142 quast_ambig_score = '0.99'
kkonganti@0 143 quast_strict_na = false
kkonganti@0 144 quast_x = 1000
kkonganti@0 145 quast_local_mis_size = 200
kkonganti@0 146 quast_sca_gap_size = 10000
kkonganti@0 147 quast_unaln_part_size = 500
kkonganti@0 148 quast_skip_unaln_mis_ctgs = false
kkonganti@0 149 quast_fragmented = false
kkonganti@0 150 quast_frag_max_ident = (params.quast_fragmented ? 200 : false)
kkonganti@0 151 quast_plots_format = 'pdf'
kkonganti@0 152 prodka_run = true
kkonganti@0 153 prodigal_run = (params.prodka_run ?: false)
kkonganti@0 154 prodigal_c = false
kkonganti@0 155 prodigal_f = 'gbk'
kkonganti@0 156 prodigal_g = 11
kkonganti@0 157 prodigal_m = true
kkonganti@0 158 prodigal_n = false
kkonganti@0 159 prodigal_p = 'single'
kkonganti@0 160 prodigal_t = true
kkonganti@0 161 prokka_run = (params.prodka_run ?: false)
kkonganti@0 162 prokka_dbdir = false
kkonganti@0 163 prokka_addgenes = true
kkonganti@0 164 prokka_addmrna = true
kkonganti@0 165 prokka_locustag = false
kkonganti@0 166 prokka_increment = false
kkonganti@0 167 prokka_gffver = false
kkonganti@0 168 prokka_compliant = true
kkonganti@0 169 prokka_centre = 'CFSAN-FDA'
kkonganti@0 170 prokka_accver = false
kkonganti@0 171 prokka_genus = (params.dpubmlstpy_org.capitalize() ?: 'Cronobacter')
kkonganti@0 172 prokka_species = false
kkonganti@0 173 prokka_strain = false
kkonganti@0 174 prokka_plasmid = false
kkonganti@0 175 prokka_kingdom = false
kkonganti@0 176 prokka_gcode = false
kkonganti@0 177 prokka_usegenus = true
kkonganti@0 178 prokka_metagenome = false
kkonganti@0 179 prokka_rawproduct = false
kkonganti@0 180 prokka_cdsrnaolap = false
kkonganti@0 181 prokka_evalue = '1e-9'
kkonganti@0 182 prokka_coverage = 80
kkonganti@0 183 prokka_fast = false
kkonganti@0 184 prokka_noanno = false
kkonganti@0 185 prokka_mincontiglen = 200
kkonganti@0 186 prokka_rfam = false
kkonganti@0 187 prokka_norrna = false
kkonganti@0 188 prokka_notrna = false
kkonganti@0 189 prokka_rnammer = false
kkonganti@0 190 pirate_run = false
kkonganti@0 191 pirate_steps = false
kkonganti@0 192 pirate_features = false
kkonganti@0 193 pirate_nucl = false
kkonganti@0 194 pirate_pan_opt = "'--diamond'"
kkonganti@0 195 pirate_pan_off = false
kkonganti@0 196 pirate_min_len = 200
kkonganti@0 197 pirate_para_off = false
kkonganti@0 198 pirate_para_args = false
kkonganti@0 199 pirate_classify_off = false
kkonganti@0 200 pirate_align = false
kkonganti@0 201 pirate_rplots = false
kkonganti@0 202 mashscreen_run = true
kkonganti@0 203 mash_sketch = (params.cronology_root_dbdir
kkonganti@0 204 + File.separator
kkonganti@0 205 + 'mash_paste'
kkonganti@0 206 + File.separator
kkonganti@0 207 + 'msh.k21.1000h.'
kkonganti@0 208 + getPDGRelease(params.cronology_root_dbdir)
kkonganti@0 209 + '.msh')
kkonganti@0 210 mlst_run = true
kkonganti@0 211 mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
kkonganti@0 212 mlst_legacy = true
kkonganti@0 213 mlst_minid = 95
kkonganti@0 214 mlst_mincov = 10
kkonganti@0 215 mlst_minscore = 50
kkonganti@0 216 mlst_blastdb = false
kkonganti@0 217 mlst_datadir = false
kkonganti@0 218 mlst_label = true
kkonganti@0 219 abricate_run = true
kkonganti@0 220 abricate_datadir = ("${projectDir}"
kkonganti@0 221 + File.separator
kkonganti@0 222 + 'assets'
kkonganti@0 223 + File.separator
kkonganti@0 224 + 'abricate_dbs')
kkonganti@0 225 abricate_minid = 90
kkonganti@0 226 abricate_mincov = 80
kkonganti@0 227 abricate_summary_run = true
kkonganti@0 228 fq_filter_by_len = 0
kkonganti@0 229 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
kkonganti@0 230 fq2_suffix = '_R2_001.fastq.gz'
kkonganti@0 231 }
kkonganti@0 232
kkonganti@0 233 /*
kkonganti@0 234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 235 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
kkonganti@0 236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 237 */
kkonganti@0 238
kkonganti@0 239 def getPDGRelease(db_path) {
kkonganti@0 240 db_path_obj = new File( db_path )
kkonganti@0 241 def pdg_release = []
kkonganti@0 242
kkonganti@0 243 db_path_obj.eachDirRecurse {
kkonganti@0 244 it.toString() =~ /PDG/ \
kkonganti@0 245 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
kkonganti@0 246 : null
kkonganti@0 247 }
kkonganti@0 248
kkonganti@0 249 return pdg_release.unique().join('').toString()
kkonganti@0 250 }