--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/workflows/conf/centriflaken.config	Wed Jul 03 15:16:39 2024 -0400
@@ -0,0 +1,59 @@
+params {
+    workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
+    workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
+    workflow_version = '0.2.1'
+    centrifuge_x = '/galaxy/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
+    centrifuge_extract_bug = 'Escherichia coli'
+    centrifuge_save_aligned = false
+    centrifuge_save_unaligned = false
+    centrifuge_out_fmt_sam = false
+    centrifuge_ignore_quals = false
+    kraken2_db = '/galaxy/cfsan-centriflaken-db/0/kraken2/standard-210914'
+    kraken2_confidence = '0.0'
+    kraken2_quick = false
+    kraken2_use_mpa_style = false
+    kraken2_minimum_base_quality = '0'
+    kraken2_report_zero_counts = false
+    kraken2_report_minimizer_data = false
+    kraken2_use_names = true
+    kraken2_extract_bug = params.centrifuge_extract_bug
+    flye_pacbio_raw = false
+    flye_pacbio_corr = false
+    flye_pacbio_hifi = false
+    flye_nano_raw = true
+    flye_nano_corr = false
+    flye_nano_hq = false
+    flye_genome_size = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? '5m' : '5.5m')
+    flye_polish_iter = false
+    flye_min_overlap = false
+    flye_scaffold = false
+    flye_meta = true
+    ectyper_run = false
+    ectyper_perc_opid = 90
+    ectyper_perc_hpid = 95
+    ectyper_perc_opcov = 95
+    ectyper_perc_hpcov = 50
+    serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
+    serotypefinder_db = '/galaxy/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
+    serotypefinder_min_cov = 0.80
+    serotypefinder_min_threshold = 0.85
+    serotypefinder_x = true
+    seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
+    seqsero2_t = 4
+    seqsero2_m = 'k'
+    seqsero2_c = false
+    seqsero2_s = false
+    mlst_run = true
+    mlst_minid = 95
+    mlst_mincov = 10
+    mlst_minscore = 50
+    amrfinderplus_run = false
+    amrfinderplus_db = '/galaxy/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
+    amrfinderplus_genes = true
+    abricate_run = true
+    abricate_datadir = '/galaxy/cfsan-centriflaken-db/0/abricate/1.0.1/db'
+    abricate_minid = 90
+    abricate_mincov = 80
+    abricate_summary_run = true
+    seqkit_grep_on = false
+}
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