kkonganti@105: params {
kkonganti@105:     workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
kkonganti@105:     workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
kkonganti@105:     workflow_version = '0.4.0'
kkonganti@105:     seqkit_rmdup_run = false
kkonganti@105:     seqkit_rmdup_n = false
kkonganti@105:     seqkit_rmdup_s = true
kkonganti@105:     seqkit_rmdup_d = false
kkonganti@105:     seqkit_rmdup_D = false
kkonganti@105:     seqkit_rmdup_P = false
kkonganti@105:     seqkit_rmdup_i = false
kkonganti@111:     centrifuge_x = '/galaxy/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
kkonganti@105:     centrifuge_extract_bug = 'Escherichia coli'
kkonganti@105:     centrifuge_save_aligned = false
kkonganti@105:     centrifuge_save_unaligned = false
kkonganti@105:     centrifuge_out_fmt_sam = false
kkonganti@105:     centrifuge_ignore_quals = false
kkonganti@111:     kraken2_db = '/galaxy/cfsan-centriflaken-db/0/kraken2/standard-210914'
kkonganti@105:     kraken2_confidence = '0.0'
kkonganti@105:     kraken2_quick = false
kkonganti@105:     kraken2_use_mpa_style = false
kkonganti@105:     kraken2_minimum_base_quality = '0'
kkonganti@105:     kraken2_report_zero_counts = false
kkonganti@105:     kraken2_report_minimizer_data = false
kkonganti@105:     kraken2_use_names = true
kkonganti@105:     kraken2_extract_bug = params.centrifuge_extract_bug
kkonganti@105:     megahit_run = true
kkonganti@105:     megahit_min_count = false
kkonganti@105:     megahit_k_list = false
kkonganti@105:     megahit_no_mercy = false
kkonganti@105:     megahit_bubble_level = false
kkonganti@105:     megahit_merge_level = false
kkonganti@105:     megahit_prune_level = false
kkonganti@105:     megahit_prune_depth = false
kkonganti@105:     megahit_low_local_ratio = false
kkonganti@105:     megahit_max_tip_len = false
kkonganti@105:     megahit_no_local = false
kkonganti@105:     megahit_kmin_1pass = false
kkonganti@105:     megahit_preset = 'meta-sensitive'
kkonganti@105:     megahit_mem_flag = 2
kkonganti@105:     megahit_min_contig_len = false
kkonganti@105:     spades_run = false
kkonganti@105:     spades_isolate = false
kkonganti@105:     spades_sc = false
kkonganti@105:     spades_meta = true
kkonganti@105:     spades_bio = false
kkonganti@105:     spades_corona = false
kkonganti@105:     spades_rna = false
kkonganti@105:     spades_plasmid = false
kkonganti@105:     spades_metaviral = false
kkonganti@105:     spades_metaplasmid = false
kkonganti@105:     spades_rnaviral = false
kkonganti@105:     spades_iontorrent = false
kkonganti@105:     spades_only_assembler = false
kkonganti@105:     spades_careful = false
kkonganti@105:     spades_cov_cutoff = false
kkonganti@105:     spades_k = false
kkonganti@105:     spades_hmm = false
kkonganti@105:     ectyper_run = false
kkonganti@105:     ectyper_perc_opid = 90
kkonganti@105:     ectyper_perc_hpid = 95
kkonganti@105:     ectyper_perc_opcov = 95
kkonganti@105:     ectyper_perc_hpcov = 50
kkonganti@105:     serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
kkonganti@111:     serotypefinder_db = '/galaxy/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
kkonganti@105:     serotypefinder_min_cov = 0.80
kkonganti@105:     serotypefinder_min_threshold = 0.85
kkonganti@105:     serotypefinder_x = true
kkonganti@105:     seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
kkonganti@105:     seqsero2_t = 4
kkonganti@105:     seqsero2_m = 'k'
kkonganti@105:     seqsero2_c = false
kkonganti@105:     seqsero2_s = false
kkonganti@105:     mlst_run = true
kkonganti@105:     mlst_minid = 95
kkonganti@105:     mlst_mincov = 10
kkonganti@105:     mlst_minscore = 50
kkonganti@105:     amrfinderplus_run = false
kkonganti@111:     amrfinderplus_db = '/galaxy/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
kkonganti@105:     amrfinderplus_genes = true
kkonganti@105:     abricate_run = true
kkonganti@111:     abricate_datadir = '/galaxy/cfsan-centriflaken-db/0/abricate/1.0.1/db'
kkonganti@105:     abricate_minid = 90
kkonganti@105:     abricate_mincov = 80
kkonganti@105:     abricate_summary_run = true
kkonganti@105:     seqkit_grep_on = false
kkonganti@105:     fq_filter_by_len = 75
kkonganti@105:     fq_suffix = '_R1_001.fastq.gz'
kkonganti@105:     fq2_suffix = '_R2_001.fastq.gz'
kkonganti@105: }