--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1.0.0/workflows/conf/bettercallsal_lr.config	Thu May 28 20:41:10 2026 +0000
@@ -0,0 +1,172 @@
+params {
+    workflow_conceived_by = 'Kranti Konganti'
+    workflow_built_by = 'Kranti Konganti'
+    workflow_version = '1.0.0'
+    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'
+    filtlong_run = true
+    filtlong_keep_perc = false
+    filtlong_target_bases = false
+    filtlong_min_length = 1000
+    filtlong_max_length = 20000
+    filtlong_min_mean_q = 75
+    filtlong_min_window_q = 75
+    filtlong_a = false
+    filtlong_1 = false
+    filtlong_2 = false
+    filtlong_len_weight = false
+    filtlong_mean_q_weight = 30
+    filtlong_window_q_weight = 30
+    filtlong_trim = false
+    filtlong_split = false
+    filtlong_window_size = 250
+    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
+    tuspy_skip = 'PRJNA766315,PRJNA675435,PRJNA831577,PRJNA855361'
+    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,k=81,k=91,k=101'
+    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 = 81
+    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 = 81
+    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 : 0.05)
+    sfhpy_gt = true
+    sfhpy_lt = false
+    salmonalign_libtype = 'U'
+    flye_run = true
+    flye_pacbio_raw = false
+    flye_pacbio_corr = false
+    flye_pacbio_hifi = false
+    flye_nano_raw = false
+    flye_nano_corr = true
+    flye_nano_hq = false
+    flye_genome_size = false
+    flye_polish_iter = '3'
+    flye_min_overlap = false
+    flye_scaffold = false
+    flye_meta = true
+    mm2_align_bam = true
+    mm2_align_bam_sorted = false
+    mm2_align_cigar_paf = false
+    mm2_align_cigar_bam = false
+    mlst_run = true
+    mlst_scheme = 'senterica_achtman_2'
+    mlst_legacy = true
+    mlst_minid = 95
+    mlst_mincov = 10
+    mlst_minscore = 50
+    abricate_run = true
+    abricate_datadir = ("${projectDir}"
+        + File.separator
+        + 'assets'
+        + File.separator
+        + 'abricate_dbs')
+    abricate_minid = 90
+    abricate_mincov = 80
+    abricate_summary_run = true
+    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_filename_delim_idx = 3
+    fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
+    fq2_suffix = '_R2_001.fastq.gz'
+    multiqc_run = true
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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()
+}