kkonganti@0: params {
kkonganti@0:     workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
kkonganti@0:     workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
kkonganti@0:     workflow_version = '0.2.0'
kkonganti@0:     centrifuge_x = '/nfs/home/galaxy/cfsan-centriflaken-db/centrifuge/2022-04-12/ab'
kkonganti@0:     centrifuge_extract_bug = 'Escherichia coli'
kkonganti@0:     centrifuge_save_aligned = false
kkonganti@0:     centrifuge_save_unaligned = false
kkonganti@0:     centrifuge_out_fmt_sam = false
kkonganti@0:     centrifuge_ignore_quals = false
kkonganti@0:     kraken2_db = '/nfs/home/galaxy/cfsan-centriflaken-db/kraken2/standard-210914'
kkonganti@0:     kraken2_confidence = '0.0'
kkonganti@0:     kraken2_quick = false
kkonganti@0:     kraken2_use_mpa_style = false
kkonganti@0:     kraken2_minimum_base_quality = '0'
kkonganti@0:     kraken2_report_zero_counts = false
kkonganti@0:     kraken2_report_minimizer_data = false
kkonganti@0:     kraken2_use_names = true
kkonganti@0:     kraken2_extract_bug = params.centrifuge_extract_bug
kkonganti@0:     flye_pacbio_raw = false
kkonganti@0:     flye_pacbio_corr = false
kkonganti@0:     flye_pacbio_hifi = false
kkonganti@0:     flye_nano_raw = true
kkonganti@0:     flye_nano_corr = false
kkonganti@0:     flye_nano_hq = false
kkonganti@0:     flye_genome_size = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? '5m' : '5.5m')
kkonganti@0:     flye_polish_iter = false
kkonganti@0:     flye_min_overlap = false
kkonganti@0:     flye_scaffold = false
kkonganti@0:     flye_meta = true
kkonganti@0:     ectyper_run = false
kkonganti@0:     ectyper_perc_opid = 90
kkonganti@0:     ectyper_perc_hpid = 95
kkonganti@0:     ectyper_perc_opcov = 95
kkonganti@0:     ectyper_perc_hpcov = 50
kkonganti@0:     serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
kkonganti@0:     serotypefinder_db = '/nfs/home/galaxy/cfsan-centriflaken-db/serotypefinder/2.0.2'
kkonganti@0:     serotypefinder_min_cov = 0.80
kkonganti@0:     serotypefinder_min_threshold = 0.85
kkonganti@0:     serotypefinder_x = true
kkonganti@0:     seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
kkonganti@0:     seqsero2_t = 4
kkonganti@0:     seqsero2_m = 'k'
kkonganti@0:     seqsero2_c = false
kkonganti@0:     seqsero2_s = false
kkonganti@0:     mlst_run = true
kkonganti@0:     mlst_minid = 95
kkonganti@0:     mlst_mincov = 10
kkonganti@0:     mlst_minscore = 50
kkonganti@0:     amrfinderplus_run = false
kkonganti@0:     amrfinderplus_db = '/nfs/home/galaxy/cfsan-centriflaken-db/amrfinderplus/3.10.24/latest'
kkonganti@0:     amrfinderplus_genes = true
kkonganti@0:     abricate_run = true
kkonganti@0:     abricate_datadir = '/nfs/home/galaxy/cfsan-centriflaken-db/abricate/1.0.1/db'
kkonganti@0:     abricate_minid = 90
kkonganti@0:     abricate_mincov = 80
kkonganti@0:     abricate_summary_run = true
kkonganti@0:     seqkit_grep_on = false
kkonganti@0: }