--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/workflows/conf/centriflaken_hy.config	Wed Jul 03 15:16:39 2024 -0400
@@ -0,0 +1,90 @@
+params {
+    workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
+    workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
+    workflow_version = '0.4.0'
+    seqkit_rmdup_run = false
+    seqkit_rmdup_n = false
+    seqkit_rmdup_s = true
+    seqkit_rmdup_d = false
+    seqkit_rmdup_D = false
+    seqkit_rmdup_P = false
+    seqkit_rmdup_i = false
+    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
+    megahit_run = true
+    megahit_min_count = false
+    megahit_k_list = false
+    megahit_no_mercy = false
+    megahit_bubble_level = false
+    megahit_merge_level = false
+    megahit_prune_level = false
+    megahit_prune_depth = false
+    megahit_low_local_ratio = false
+    megahit_max_tip_len = false
+    megahit_no_local = false
+    megahit_kmin_1pass = false
+    megahit_preset = 'meta-sensitive'
+    megahit_mem_flag = 2
+    megahit_min_contig_len = false
+    spades_run = false
+    spades_isolate = false
+    spades_sc = false
+    spades_meta = true
+    spades_bio = false
+    spades_corona = false
+    spades_rna = false
+    spades_plasmid = false
+    spades_metaviral = false
+    spades_metaplasmid = false
+    spades_rnaviral = false
+    spades_iontorrent = false
+    spades_only_assembler = false
+    spades_careful = false
+    spades_cov_cutoff = false
+    spades_k = false
+    spades_hmm = false
+    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
+    fq_filter_by_len = 75
+    fq_suffix = '_R1_001.fastq.gz'
+    fq2_suffix = '_R2_001.fastq.gz'
+}
\ No newline at end of file