--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/workflows/conf/bettercallsal.config	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,253 @@
+params {
+    workflow_conceived_by = 'Kranti Konganti'
+    workflow_built_by = 'Kranti Konganti'
+    workflow_version = '0.5.0'
+    bcs_root_dbdir = '/tool/tool-data/cfsan_bettercallsal_db/latest'
+    bcs_db_mode = 'snp'
+    bcs_db_mode_index = (params.bcs_db_mode ==~ /snp/ ? '_cluster' : '_serotype')
+    bcs_thresholds = 'strict'
+    bcs_concat_pe = true
+    bbmerge_run = (params.bcs_concat_pe ? false : true)
+    bbmerge_adapters = false
+    bbmerge_reads = -1
+    bbmerge_ziplevel = 1
+    bbmerge_ordered = false
+    bbmerge_qtrim = true
+    bbmerge_qtrim2 = false
+    bbmerge_trimq = 10
+    bbmerge_minlength = 1
+    bbmerge_tbo = false
+    bbmerge_minavgquality = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
+    bbmerge_trimpolya = true
+    bbmerge_pfilter = (params.bcs_thresholds ==~ /strict/ ? 1 : false)
+    bbmerge_ouq = false
+    bbmerge_owq = true
+    bbmerge_strict = false
+    bbmerge_verystrict = false 
+    bbmerge_ultrastrict = (params.bcs_thresholds ==~ /strict/ ? true : false)
+    bbmerge_maxstrict = false
+    bbmerge_loose = false
+    bbmerge_veryloose = false
+    bbmerge_ultraloose = false
+    bbmerge_maxloose = false
+    bbmerge_fast = false
+    bbmerge_k = 60
+    bbmerge_prealloc = true
+    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_run = true
+    mash_sketch = (params.bcs_root_dbdir 
+        + File.separator 
+        + 'mash_sketch' 
+        + File.separator 
+        + 'msh.k21.1000h.' 
+        + params.bcs_db_mode 
+        + '.msh')
+    mashscreen_w = false
+    mashscreen_i = false
+    mashscreen_v = false
+    tuspy_run = true
+    tuspy_s = false
+    tuspy_m = false
+    tuspy_ps = (params.bcs_root_dbdir 
+        + File.separator 
+        + 'index_metadata' 
+        + File.separator 
+        + 'per_' 
+        + params.bcs_db_mode 
+        + params.bcs_db_mode_index 
+        + '.ACC2SERO.pickle')
+    tuspy_gd = (params.bcs_root_dbdir 
+        + File.separator 
+        + 'scaffold_genomes')
+    tuspy_gds = '_scaffolded_genomic.fna.gz'
+    tuspy_n = 10
+    sourmashsketch_run = true
+    sourmashsketch_mode = 'dna'
+    sourmashsketch_file = false
+    sourmashsketch_f = false
+    sourmashsketch_merge = false
+    sourmashsketch_name = false
+    sourmashsketch_p = 'abund,scaled=1000,k=51,k=61,k=71'
+    sourmashsketch_singleton = true
+    sourmashsketch_randomize = false
+    sourmashgather_run = (params.sourmashsketch_run ?: false)
+    sourmashgather_n = false
+    sourmashgather_thr_bp = false
+    sourmashgather_ignoreabn = false
+    sourmashgather_prefetch = false
+    sourmashgather_noprefetch = false
+    sourmashgather_ani_ci = true
+    sourmashgather_k = 71
+    sourmashgather_protein = false
+    sourmashgather_noprotein = false
+    sourmashgather_dayhoff = false
+    sourmashgather_nodayhoff = false
+    sourmashgather_hp = false
+    sourmashgather_nohp = false
+    sourmashgather_dna = true
+    sourmashgather_nodna = false
+    sourmashgather_scaled = false
+    sourmashgather_inc_pat = false
+    sourmashgather_exc_pat = false
+    sourmashsearch_run = (params.sourmashsketch_run && !params.sourmashgather_run ?: false)
+    sourmashsearch_n = false
+    sourmashsearch_thr = '0'
+    sourmashsearch_contain = false
+    sourmashsearch_maxcontain = true
+    sourmashsearch_ignoreabn = true
+    sourmashsearch_ani_ci = false
+    sourmashsearch_k = 71
+    sourmashsearch_protein = false
+    sourmashsearch_noprotein = false
+    sourmashsearch_dayhoff = false
+    sourmashsearch_nodayhoff = false
+    sourmashsearch_hp = false
+    sourmashsearch_nohp = false
+    sourmashsearch_dna = true
+    sourmashsearch_nodna = false
+    sourmashsearch_scaled = false
+    sourmashsearch_inc_pat = false
+    sourmashsearch_exc_pat = false
+    sfhpy_run = true
+    sfhpy_fcn = (params.sourmashsearch_run ? 'similarity' : 'f_match')
+    sfhpy_fcv = (params.sourmashsearch_run ? 0.9 : 0.1)
+    sfhpy_gt = true
+    sfhpy_lt = false
+    kmaindex_run = true
+    kmaindex_t_db = false
+    kmaindex_k = 31
+    kmaindex_m = false
+    kmaindex_hc = false
+    kmaindex_ML = false
+    kmaindex_ME = false
+    kmaindex_Sparse = false
+    kmaindex_ht = false
+    kmaindex_hq = false
+    kmaindex_and = false
+    kmaindex_nbp = false
+    kmaalign_run = true
+    kmaalign_ignorequals = false
+    kmaalign_int = false
+    kmaalign_ef = false
+    kmaalign_vcf = false
+    kmaalign_sam = false
+    kmaalign_nc = true
+    kmaalign_na = true
+    kmaalign_nf = true
+    kmaalign_a = false
+    kmaalign_and = true
+    kmaalign_oa = false
+    kmaalign_bc = false
+    kmaalign_bcNano = false
+    kmaalign_bcd = false
+    kmaalign_bcg = false
+    kmaalign_ID = (params.bcs_thresholds ==~ /strict/ ? 10.0 : 5.0)
+    kmaalign_md = false
+    kmaalign_dense = false
+    kmaalign_ref_fsa = false
+    kmaalign_Mt1 = false
+    kmaalign_1t1 = false
+    kmaalign_mrs = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
+    kmaalign_mrc = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
+    kmaalign_mp = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
+    kmaalign_eq = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
+    kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
+    kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
+    kmaalign_mq = false
+    kmaalign_5p = false
+    kmaalign_3p = false
+    kmaalign_apm = false
+    kmaalign_cge = false
+    kmaalign_mrs = (params.sourmashgather_run ? false : params.kmaalign_mrs)
+    kmaalign_and = (params.sourmashgather_run ? false : true)
+    kmaalign_ID = (params.sourmashgather_run ? false : params.kmaalign_ID)
+    salmonidx_run = true
+    salmonidx_k = false
+    salmonidx_gencode = false
+    salmonidx_features = false
+    salmonidx_keepDuplicates = false
+    salmonidx_keepFixedFasta = false
+    salmonidx_filterSize = false
+    salmonidx_sparse = false
+    salmonidx_n = false
+    salmonidx_decoys = false
+    salmonalign_libtype = 'SF'
+    gsrpy_run = true
+    gsrpy_url = true
+    gsrpy_snp_clus_metadata =  (params.bcs_root_dbdir
+        + File.separator
+        + 'download_pdg_metadata'
+        + File.separator 
+        + getPDGRelease(params.bcs_root_dbdir) 
+        + File.separator
+        + getPDGRelease(params.bcs_root_dbdir) 
+        + '.reference_target.cluster_list.tsv')
+    sourmashcompare_mode = 'ani,containment'
+    fq_filter_by_len = 0
+    fq_suffix = '.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()
+}