kkonganti@11: params {
kkonganti@11:     workflow_conceived_by = 'Kranti Konganti'
kkonganti@11:     workflow_built_by = 'Kranti Konganti'
kkonganti@11:     workflow_version = '0.6.1'
kkonganti@12:     bcs_root_dbdir = '/tool/tool-data/cfsan_bettercallsal_db/latest'
kkonganti@11:     bcs_db_mode = 'snp'
kkonganti@11:     bcs_db_mode_index = (params.bcs_db_mode ==~ /snp/ ? '_cluster' : '_serotype')
kkonganti@11:     bcs_thresholds = 'strict'
kkonganti@11:     bcs_concat_pe = true
kkonganti@11:     bbmerge_run = (params.bcs_concat_pe ? false : true)
kkonganti@11:     bbmerge_adapters = false
kkonganti@11:     bbmerge_reads = -1
kkonganti@11:     bbmerge_ziplevel = 1
kkonganti@11:     bbmerge_ordered = false
kkonganti@11:     bbmerge_qtrim = true
kkonganti@11:     bbmerge_qtrim2 = false
kkonganti@11:     bbmerge_trimq = 10
kkonganti@11:     bbmerge_minlength = 1
kkonganti@11:     bbmerge_tbo = false
kkonganti@11:     bbmerge_minavgquality = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
kkonganti@11:     bbmerge_trimpolya = true
kkonganti@11:     bbmerge_pfilter = (params.bcs_thresholds ==~ /strict/ ? 1 : false)
kkonganti@11:     bbmerge_ouq = false
kkonganti@11:     bbmerge_owq = true
kkonganti@11:     bbmerge_strict = false
kkonganti@11:     bbmerge_verystrict = false 
kkonganti@11:     bbmerge_ultrastrict = (params.bcs_thresholds ==~ /strict/ ? true : false)
kkonganti@11:     bbmerge_maxstrict = false
kkonganti@11:     bbmerge_loose = false
kkonganti@11:     bbmerge_veryloose = false
kkonganti@11:     bbmerge_ultraloose = false
kkonganti@11:     bbmerge_maxloose = false
kkonganti@11:     bbmerge_fast = false
kkonganti@11:     bbmerge_k = 60
kkonganti@11:     bbmerge_prealloc = true
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_run = true
kkonganti@11:     mash_sketch = (params.bcs_root_dbdir 
kkonganti@11:         + File.separator 
kkonganti@11:         + 'mash_sketch' 
kkonganti@11:         + File.separator 
kkonganti@11:         + 'msh.k21.1000h.' 
kkonganti@11:         + params.bcs_db_mode 
kkonganti@11:         + '.msh')
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.bcs_root_dbdir 
kkonganti@11:         + File.separator 
kkonganti@11:         + 'index_metadata' 
kkonganti@11:         + File.separator 
kkonganti@11:         + 'per_' 
kkonganti@11:         + params.bcs_db_mode 
kkonganti@11:         + params.bcs_db_mode_index 
kkonganti@11:         + '.ACC2SERO.pickle')
kkonganti@11:     tuspy_gd = (params.bcs_root_dbdir 
kkonganti@11:         + File.separator 
kkonganti@11:         + 'scaffold_genomes')
kkonganti@11:     tuspy_gds = '_scaffolded_genomic.fna.gz'
kkonganti@11:     tuspy_n = 10
kkonganti@11:     sourmashsketch_run = true
kkonganti@11:     sourmashsketch_mode = 'dna'
kkonganti@11:     sourmashsketch_file = false
kkonganti@11:     sourmashsketch_f = false
kkonganti@11:     sourmashsketch_merge = false
kkonganti@11:     sourmashsketch_name = false
kkonganti@11:     sourmashsketch_p = 'abund,scaled=1000,k=51,k=61,k=71'
kkonganti@11:     sourmashsketch_singleton = true
kkonganti@11:     sourmashsketch_randomize = false
kkonganti@11:     sourmashgather_run = (params.sourmashsketch_run ?: false)
kkonganti@11:     sourmashgather_n = false
kkonganti@11:     sourmashgather_thr_bp = false
kkonganti@11:     sourmashgather_ignoreabn = false
kkonganti@11:     sourmashgather_prefetch = false
kkonganti@11:     sourmashgather_noprefetch = false
kkonganti@11:     sourmashgather_ani_ci = true
kkonganti@11:     sourmashgather_k = 71
kkonganti@11:     sourmashgather_protein = false
kkonganti@11:     sourmashgather_noprotein = false
kkonganti@11:     sourmashgather_dayhoff = false
kkonganti@11:     sourmashgather_nodayhoff = false
kkonganti@11:     sourmashgather_hp = false
kkonganti@11:     sourmashgather_nohp = false
kkonganti@11:     sourmashgather_dna = true
kkonganti@11:     sourmashgather_nodna = false
kkonganti@11:     sourmashgather_scaled = false
kkonganti@11:     sourmashgather_inc_pat = false
kkonganti@11:     sourmashgather_exc_pat = false
kkonganti@11:     sourmashsearch_run = (params.sourmashsketch_run && !params.sourmashgather_run ?: false)
kkonganti@11:     sourmashsearch_n = false
kkonganti@11:     sourmashsearch_thr = '0'
kkonganti@11:     sourmashsearch_contain = false
kkonganti@11:     sourmashsearch_maxcontain = true
kkonganti@11:     sourmashsearch_ignoreabn = true
kkonganti@11:     sourmashsearch_ani_ci = false
kkonganti@11:     sourmashsearch_k = 71
kkonganti@11:     sourmashsearch_protein = false
kkonganti@11:     sourmashsearch_noprotein = false
kkonganti@11:     sourmashsearch_dayhoff = false
kkonganti@11:     sourmashsearch_nodayhoff = false
kkonganti@11:     sourmashsearch_hp = false
kkonganti@11:     sourmashsearch_nohp = false
kkonganti@11:     sourmashsearch_dna = true
kkonganti@11:     sourmashsearch_nodna = false
kkonganti@11:     sourmashsearch_scaled = false
kkonganti@11:     sourmashsearch_inc_pat = false
kkonganti@11:     sourmashsearch_exc_pat = false
kkonganti@11:     sfhpy_run = true
kkonganti@11:     sfhpy_fcn = (params.sourmashsearch_run ? 'similarity' : 'f_match')
kkonganti@11:     sfhpy_fcv = (params.sourmashsearch_run ? 0.9 : 0.1)
kkonganti@11:     sfhpy_gt = true
kkonganti@11:     sfhpy_lt = false
kkonganti@11:     kmaindex_run = true
kkonganti@11:     kmaindex_t_db = false
kkonganti@11:     kmaindex_k = 31
kkonganti@11:     kmaindex_m = false
kkonganti@11:     kmaindex_hc = false
kkonganti@11:     kmaindex_ML = false
kkonganti@11:     kmaindex_ME = false
kkonganti@11:     kmaindex_Sparse = false
kkonganti@11:     kmaindex_ht = false
kkonganti@11:     kmaindex_hq = false
kkonganti@11:     kmaindex_and = false
kkonganti@11:     kmaindex_nbp = false
kkonganti@11:     kmaalign_run = true
kkonganti@11:     kmaalign_ignorequals = false
kkonganti@11:     kmaalign_int = false
kkonganti@11:     kmaalign_ef = false
kkonganti@11:     kmaalign_vcf = false
kkonganti@11:     kmaalign_sam = false
kkonganti@11:     kmaalign_nc = true
kkonganti@11:     kmaalign_na = true
kkonganti@11:     kmaalign_nf = false
kkonganti@11:     kmaalign_a = false
kkonganti@11:     kmaalign_and = true
kkonganti@11:     kmaalign_oa = false
kkonganti@11:     kmaalign_bc = false
kkonganti@11:     kmaalign_bcNano = false
kkonganti@11:     kmaalign_bcd = false
kkonganti@11:     kmaalign_bcg = false
kkonganti@11:     kmaalign_ID = (params.bcs_thresholds ==~ /strict/ ? 10.0 : 5.0)
kkonganti@11:     kmaalign_md = false
kkonganti@11:     kmaalign_dense = false
kkonganti@11:     kmaalign_ref_fsa = false
kkonganti@11:     kmaalign_Mt1 = false
kkonganti@11:     kmaalign_1t1 = false
kkonganti@11:     kmaalign_mrs = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
kkonganti@11:     kmaalign_mrc = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
kkonganti@11:     kmaalign_mp = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
kkonganti@11:     kmaalign_eq = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
kkonganti@11:     kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
kkonganti@11:     kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
kkonganti@11:     kmaalign_mq = false
kkonganti@11:     kmaalign_5p = false
kkonganti@11:     kmaalign_3p = false
kkonganti@11:     kmaalign_apm = false
kkonganti@11:     kmaalign_cge = false
kkonganti@11:     kmaalign_mrs = (params.sourmashgather_run ? false : params.kmaalign_mrs)
kkonganti@11:     kmaalign_and = (params.sourmashgather_run ? false : true)
kkonganti@11:     kmaalign_ID = (params.sourmashgather_run ? false : params.kmaalign_ID)
kkonganti@11:     megahit_run = true
kkonganti@11:     megahit_min_count = false
kkonganti@11:     megahit_k_list = false
kkonganti@11:     megahit_no_mercy = false
kkonganti@11:     megahit_bubble_level = false
kkonganti@11:     megahit_merge_level = false
kkonganti@11:     megahit_prune_level = false
kkonganti@11:     megahit_prune_depth = false
kkonganti@11:     megahit_low_local_ratio = false
kkonganti@11:     megahit_max_tip_len = false
kkonganti@11:     megahit_no_local = false
kkonganti@11:     megahit_kmin_1pass = false
kkonganti@11:     megahit_preset = 'meta-sensitive'
kkonganti@11:     megahit_mem_flag = 2
kkonganti@11:     megahit_min_contig_len = false
kkonganti@11:     mlst_run = true
kkonganti@11:     mlst_scheme = 'senterica_achtman_2'
kkonganti@11:     mlst_legacy = true
kkonganti@11:     mlst_minid = 95
kkonganti@11:     mlst_mincov = 10
kkonganti@11:     mlst_minscore = 50
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:     salmonidx_run = true
kkonganti@11:     salmonidx_k = false
kkonganti@11:     salmonidx_gencode = false
kkonganti@11:     salmonidx_features = false
kkonganti@11:     salmonidx_keepDuplicates = false
kkonganti@11:     salmonidx_keepFixedFasta = false
kkonganti@11:     salmonidx_filterSize = false
kkonganti@11:     salmonidx_sparse = false
kkonganti@11:     salmonidx_n = false
kkonganti@11:     salmonidx_decoys = false
kkonganti@11:     salmonalign_libtype = 'SF'
kkonganti@11:     gsrpy_run = true
kkonganti@11:     gsrpy_url = true
kkonganti@11:     gsrpy_snp_clus_metadata =  (params.bcs_root_dbdir
kkonganti@11:         + File.separator
kkonganti@11:         + 'download_pdg_metadata'
kkonganti@11:         + File.separator 
kkonganti@11:         + getPDGRelease(params.bcs_root_dbdir) 
kkonganti@11:         + File.separator
kkonganti@11:         + getPDGRelease(params.bcs_root_dbdir) 
kkonganti@11:         + '.reference_target.cluster_list.tsv')
kkonganti@11:     sourmashcompare_mode = 'ani,containment'
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: }