Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.7.0/workflows/conf/bettercallsal.config @ 18:75558ffe3e68

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 11:01:13 -0400
parents 0e7a0053e4a6
children
rev   line source
kkonganti@17 1 params {
kkonganti@17 2 workflow_conceived_by = 'Kranti Konganti'
kkonganti@17 3 workflow_built_by = 'Kranti Konganti'
kkonganti@17 4 workflow_version = '0.7.0'
kkonganti@18 5 bcs_root_dbdir = '/galaxy/cfsan-centriflaken-db/bettercallsal/PDG000000002.3082'
kkonganti@17 6 bcs_db_mode = 'snp'
kkonganti@17 7 bcs_db_mode_index = (params.bcs_db_mode ==~ /snp/ ? '_cluster' : '_serotype')
kkonganti@17 8 bcs_thresholds = 'strict'
kkonganti@17 9 bcs_concat_pe = true
kkonganti@17 10 bbmerge_run = (params.bcs_concat_pe ? false : true)
kkonganti@17 11 bbmerge_adapters = false
kkonganti@17 12 bbmerge_reads = -1
kkonganti@17 13 bbmerge_ziplevel = 1
kkonganti@17 14 bbmerge_ordered = false
kkonganti@17 15 bbmerge_qtrim = true
kkonganti@17 16 bbmerge_qtrim2 = false
kkonganti@17 17 bbmerge_trimq = 10
kkonganti@17 18 bbmerge_minlength = 1
kkonganti@17 19 bbmerge_tbo = false
kkonganti@17 20 bbmerge_minavgquality = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
kkonganti@17 21 bbmerge_trimpolya = true
kkonganti@17 22 bbmerge_pfilter = (params.bcs_thresholds ==~ /strict/ ? 1 : false)
kkonganti@17 23 bbmerge_ouq = false
kkonganti@17 24 bbmerge_owq = true
kkonganti@17 25 bbmerge_strict = false
kkonganti@17 26 bbmerge_verystrict = false
kkonganti@17 27 bbmerge_ultrastrict = (params.bcs_thresholds ==~ /strict/ ? true : false)
kkonganti@17 28 bbmerge_maxstrict = false
kkonganti@17 29 bbmerge_loose = false
kkonganti@17 30 bbmerge_veryloose = false
kkonganti@17 31 bbmerge_ultraloose = false
kkonganti@17 32 bbmerge_maxloose = false
kkonganti@17 33 bbmerge_fast = false
kkonganti@17 34 bbmerge_k = 60
kkonganti@17 35 bbmerge_prealloc = true
kkonganti@17 36 fastp_run = true
kkonganti@17 37 fastp_failed_out = false
kkonganti@17 38 fastp_merged_out = false
kkonganti@17 39 fastp_overlapped_out = false
kkonganti@17 40 fastp_6 = false
kkonganti@17 41 fastp_reads_to_process = 0
kkonganti@17 42 fastp_fix_mgi_id = false
kkonganti@17 43 fastp_A = false
kkonganti@17 44 fastp_f = 0
kkonganti@17 45 fastp_t = 0
kkonganti@17 46 fastp_b = 0
kkonganti@17 47 fastp_F = 0
kkonganti@17 48 fastp_T = 0
kkonganti@17 49 fastp_B = 0
kkonganti@17 50 fastp_dedup = true
kkonganti@17 51 fastp_dup_calc_accuracy = 6
kkonganti@17 52 fastp_poly_g_min_len = 10
kkonganti@17 53 fastp_G = true
kkonganti@17 54 fastp_x = false
kkonganti@17 55 fastp_poly_x_min_len = 10
kkonganti@17 56 fastp_cut_front = true
kkonganti@17 57 fastp_cut_tail = false
kkonganti@17 58 fastp_cut_right = true
kkonganti@17 59 fastp_W = 20
kkonganti@17 60 fastp_M = 30
kkonganti@17 61 fastp_q = 30
kkonganti@17 62 fastp_u = 40
kkonganti@17 63 fastp_n = 5
kkonganti@17 64 fastp_e = 0
kkonganti@17 65 fastp_l = 35
kkonganti@17 66 fastp_max_len = 0
kkonganti@17 67 fastp_y = true
kkonganti@17 68 fastp_Y = 30
kkonganti@17 69 fastp_U = false
kkonganti@17 70 fastp_umi_loc = false
kkonganti@17 71 fastp_umi_len = false
kkonganti@17 72 fastp_umi_prefix = false
kkonganti@17 73 fastp_umi_skip = false
kkonganti@17 74 fastp_p = true
kkonganti@17 75 fastp_P = 20
kkonganti@17 76 fastp_use_custom_adapters = false
kkonganti@17 77 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
kkonganti@17 78 + File.separator
kkonganti@17 79 + 'assets'
kkonganti@17 80 + File.separator
kkonganti@17 81 + 'adaptors.fa' : false)
kkonganti@17 82 mashscreen_run = true
kkonganti@17 83 mash_sketch = (params.bcs_root_dbdir
kkonganti@17 84 + File.separator
kkonganti@17 85 + 'mash_sketch'
kkonganti@17 86 + File.separator
kkonganti@17 87 + 'msh.k21.1000h.'
kkonganti@17 88 + params.bcs_db_mode
kkonganti@17 89 + '.msh')
kkonganti@17 90 mashscreen_w = false
kkonganti@17 91 mashscreen_i = false
kkonganti@17 92 mashscreen_v = false
kkonganti@17 93 tuspy_run = true
kkonganti@17 94 tuspy_s = false
kkonganti@17 95 tuspy_m = false
kkonganti@17 96 tuspy_ps = (params.bcs_root_dbdir
kkonganti@17 97 + File.separator
kkonganti@17 98 + 'index_metadata'
kkonganti@17 99 + File.separator
kkonganti@17 100 + 'per_'
kkonganti@17 101 + params.bcs_db_mode
kkonganti@17 102 + params.bcs_db_mode_index
kkonganti@17 103 + '.ACC2SERO.pickle')
kkonganti@17 104 tuspy_gd = (params.bcs_root_dbdir
kkonganti@17 105 + File.separator
kkonganti@17 106 + 'scaffold_genomes')
kkonganti@17 107 tuspy_gds = '_scaffolded_genomic.fna.gz'
kkonganti@17 108 tuspy_n = 10
kkonganti@17 109 tuspy_skip = 'PRJNA766315,PRJNA675435,PRJNA831577,PRJNA855361'
kkonganti@17 110 sourmashsketch_run = true
kkonganti@17 111 sourmashsketch_mode = 'dna'
kkonganti@17 112 sourmashsketch_file = false
kkonganti@17 113 sourmashsketch_f = false
kkonganti@17 114 sourmashsketch_merge = false
kkonganti@17 115 sourmashsketch_name = false
kkonganti@17 116 sourmashsketch_p = 'abund,scaled=1000,k=51,k=61,k=71'
kkonganti@17 117 sourmashsketch_singleton = true
kkonganti@17 118 sourmashsketch_randomize = false
kkonganti@17 119 sourmashgather_run = (params.sourmashsketch_run ?: false)
kkonganti@17 120 sourmashgather_n = false
kkonganti@17 121 sourmashgather_thr_bp = false
kkonganti@17 122 sourmashgather_ignoreabn = false
kkonganti@17 123 sourmashgather_prefetch = false
kkonganti@17 124 sourmashgather_noprefetch = false
kkonganti@17 125 sourmashgather_ani_ci = true
kkonganti@17 126 sourmashgather_k = 71
kkonganti@17 127 sourmashgather_protein = false
kkonganti@17 128 sourmashgather_noprotein = false
kkonganti@17 129 sourmashgather_dayhoff = false
kkonganti@17 130 sourmashgather_nodayhoff = false
kkonganti@17 131 sourmashgather_hp = false
kkonganti@17 132 sourmashgather_nohp = false
kkonganti@17 133 sourmashgather_dna = true
kkonganti@17 134 sourmashgather_nodna = false
kkonganti@17 135 sourmashgather_scaled = false
kkonganti@17 136 sourmashgather_inc_pat = false
kkonganti@17 137 sourmashgather_exc_pat = false
kkonganti@17 138 sourmashsearch_run = (params.sourmashsketch_run && !params.sourmashgather_run ?: false)
kkonganti@17 139 sourmashsearch_n = false
kkonganti@17 140 sourmashsearch_thr = '0'
kkonganti@17 141 sourmashsearch_contain = false
kkonganti@17 142 sourmashsearch_maxcontain = true
kkonganti@17 143 sourmashsearch_ignoreabn = true
kkonganti@17 144 sourmashsearch_ani_ci = false
kkonganti@17 145 sourmashsearch_k = 71
kkonganti@17 146 sourmashsearch_protein = false
kkonganti@17 147 sourmashsearch_noprotein = false
kkonganti@17 148 sourmashsearch_dayhoff = false
kkonganti@17 149 sourmashsearch_nodayhoff = false
kkonganti@17 150 sourmashsearch_hp = false
kkonganti@17 151 sourmashsearch_nohp = false
kkonganti@17 152 sourmashsearch_dna = true
kkonganti@17 153 sourmashsearch_nodna = false
kkonganti@17 154 sourmashsearch_scaled = false
kkonganti@17 155 sourmashsearch_inc_pat = false
kkonganti@17 156 sourmashsearch_exc_pat = false
kkonganti@17 157 sfhpy_run = true
kkonganti@17 158 sfhpy_fcn = (params.sourmashsearch_run ? 'similarity' : 'f_match')
kkonganti@17 159 sfhpy_fcv = (params.sourmashsearch_run ? 0.9 : 0.1)
kkonganti@17 160 sfhpy_gt = true
kkonganti@17 161 sfhpy_lt = false
kkonganti@17 162 kmaindex_run = true
kkonganti@17 163 kmaindex_t_db = false
kkonganti@17 164 kmaindex_k = 31
kkonganti@17 165 kmaindex_m = false
kkonganti@17 166 kmaindex_hc = false
kkonganti@17 167 kmaindex_ML = false
kkonganti@17 168 kmaindex_ME = false
kkonganti@17 169 kmaindex_Sparse = false
kkonganti@17 170 kmaindex_ht = false
kkonganti@17 171 kmaindex_hq = false
kkonganti@17 172 kmaindex_and = false
kkonganti@17 173 kmaindex_nbp = false
kkonganti@17 174 kmaalign_run = true
kkonganti@17 175 kmaalign_ignorequals = false
kkonganti@17 176 kmaalign_int = false
kkonganti@17 177 kmaalign_ef = false
kkonganti@17 178 kmaalign_vcf = false
kkonganti@17 179 kmaalign_sam = false
kkonganti@17 180 kmaalign_nc = true
kkonganti@17 181 kmaalign_na = true
kkonganti@17 182 kmaalign_nf = false
kkonganti@17 183 kmaalign_a = false
kkonganti@17 184 kmaalign_and = true
kkonganti@17 185 kmaalign_oa = false
kkonganti@17 186 kmaalign_bc = false
kkonganti@17 187 kmaalign_bcNano = false
kkonganti@17 188 kmaalign_bcd = false
kkonganti@17 189 kmaalign_bcg = false
kkonganti@17 190 kmaalign_ID = (params.bcs_thresholds ==~ /strict/ ? 10.0 : 5.0)
kkonganti@17 191 kmaalign_md = false
kkonganti@17 192 kmaalign_dense = false
kkonganti@17 193 kmaalign_ref_fsa = false
kkonganti@17 194 kmaalign_Mt1 = false
kkonganti@17 195 kmaalign_1t1 = false
kkonganti@17 196 kmaalign_mrs = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
kkonganti@17 197 kmaalign_mrc = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
kkonganti@17 198 kmaalign_mp = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
kkonganti@17 199 kmaalign_eq = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
kkonganti@17 200 kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
kkonganti@17 201 kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
kkonganti@17 202 kmaalign_mq = false
kkonganti@17 203 kmaalign_5p = false
kkonganti@17 204 kmaalign_3p = false
kkonganti@17 205 kmaalign_apm = false
kkonganti@17 206 kmaalign_cge = false
kkonganti@17 207 kmaalign_mrs = (params.sourmashgather_run ? false : params.kmaalign_mrs)
kkonganti@17 208 kmaalign_and = (params.sourmashgather_run ? false : true)
kkonganti@17 209 kmaalign_ID = (params.sourmashgather_run ? false : params.kmaalign_ID)
kkonganti@17 210 megahit_run = true
kkonganti@17 211 megahit_min_count = false
kkonganti@17 212 megahit_k_list = false
kkonganti@17 213 megahit_no_mercy = false
kkonganti@17 214 megahit_bubble_level = false
kkonganti@17 215 megahit_merge_level = false
kkonganti@17 216 megahit_prune_level = false
kkonganti@17 217 megahit_prune_depth = false
kkonganti@17 218 megahit_low_local_ratio = false
kkonganti@17 219 megahit_max_tip_len = false
kkonganti@17 220 megahit_no_local = false
kkonganti@17 221 megahit_kmin_1pass = false
kkonganti@17 222 megahit_preset = 'meta-sensitive'
kkonganti@17 223 megahit_mem_flag = 2
kkonganti@17 224 megahit_min_contig_len = false
kkonganti@17 225 mlst_run = true
kkonganti@17 226 mlst_scheme = 'senterica_achtman_2'
kkonganti@17 227 mlst_legacy = true
kkonganti@17 228 mlst_minid = 95
kkonganti@17 229 mlst_mincov = 10
kkonganti@17 230 mlst_minscore = 50
kkonganti@17 231 abricate_run = true
kkonganti@17 232 abricate_datadir = ("${projectDir}"
kkonganti@17 233 + File.separator
kkonganti@17 234 + 'assets'
kkonganti@17 235 + File.separator
kkonganti@17 236 + 'abricate_dbs')
kkonganti@17 237 abricate_minid = 90
kkonganti@17 238 abricate_mincov = 80
kkonganti@17 239 abricate_summary_run = true
kkonganti@17 240 salmonidx_run = true
kkonganti@17 241 salmonidx_k = false
kkonganti@17 242 salmonidx_gencode = false
kkonganti@17 243 salmonidx_features = false
kkonganti@17 244 salmonidx_keepDuplicates = false
kkonganti@17 245 salmonidx_keepFixedFasta = false
kkonganti@17 246 salmonidx_filterSize = false
kkonganti@17 247 salmonidx_sparse = false
kkonganti@17 248 salmonidx_n = false
kkonganti@17 249 salmonidx_decoys = false
kkonganti@17 250 salmonalign_libtype = 'SF'
kkonganti@17 251 gsrpy_run = true
kkonganti@17 252 gsrpy_url = true
kkonganti@17 253 gsrpy_snp_clus_metadata = (params.bcs_root_dbdir
kkonganti@17 254 + File.separator
kkonganti@17 255 + 'download_pdg_metadata'
kkonganti@17 256 + File.separator
kkonganti@17 257 + getPDGRelease(params.bcs_root_dbdir)
kkonganti@17 258 + File.separator
kkonganti@17 259 + getPDGRelease(params.bcs_root_dbdir)
kkonganti@17 260 + '.reference_target.cluster_list.tsv')
kkonganti@17 261 sourmashcompare_mode = 'ani,containment'
kkonganti@17 262 fq_filter_by_len = 0
kkonganti@17 263 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
kkonganti@17 264 fq2_suffix = '_R2_001.fastq.gz'
kkonganti@17 265 multiqc_run = true
kkonganti@17 266 }
kkonganti@17 267
kkonganti@17 268 /*
kkonganti@17 269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17 270 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
kkonganti@17 271 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17 272 */
kkonganti@17 273
kkonganti@17 274 def getPDGRelease(db_path) {
kkonganti@17 275 db_path_obj = new File( db_path )
kkonganti@17 276 def pdg_release = []
kkonganti@17 277
kkonganti@17 278 db_path_obj.eachDirRecurse {
kkonganti@17 279 it.toString() =~ /PDG/ \
kkonganti@17 280 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
kkonganti@17 281 : null
kkonganti@17 282 }
kkonganti@17 283
kkonganti@17 284 return pdg_release.unique().join('').toString()
kkonganti@17 285 }