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TheiaEuk Workflow Series

Quick Facts

Workflow Type Applicable Kingdom Last Known Changes Command-line Compatibility Workflow Level Dockstore
Genomic Characterization Mycotics vX.X.X Some optional features incompatible, Yes Sample-level TheiaEuk_Illumina_PE_PHB, TheiaEuk_ONT_PHB

TheiaEuk Workflows

The TheiaEuk workflows are for the assembly, quality assessment, and characterization of fungal genomes. It is designed to accept Illumina paired-end sequencing data or base-called ONT reads as the primary input. It is currently intended only for haploid fungal genomes like Candidozyma auris. Analyzing diploid genomes using TheiaEuk should be attempted only with expert attention to the resulting genome quality.

All input reads are processed through "core tasks" in each workflow. The core tasks include raw read quality assessment, read cleaning (quality trimming and adapter removal), de novo assembly, assembly quality assessment, and species taxon identification. For some taxa identified, taxa-specific sub-workflows will be automatically activated, undertaking additional taxa-specific characterization steps, including clade-typing and/or antifungal resistance detection.

TheiaEuk Illumina PE Workflow Diagram

TheiaEuk Illumina PE Workflow Diagram

TheiaEuk ONT Workflow Diagram

TheiaEuk ONT Workflow Diagram

Before running TheiaEuk

TheiaEuk_Illumina_PE relies on Snippy to perform variant calling on the cleaned read dataset and then queries the resulting file for specific mutations that are known to confim antifugal resistance (see Organism-specific characterization section). This behaviour has been replicated in TheiaEuk_ONT but the variant calling is performed directly on the resulting assemblies. Therefore, the read support reported is, at the moment, non-reliable. Future improvements will include improvements on this module.

Inputs

Input Read Data

The TheiaEuk_Illumina_PE workflow takes in Illumina paired-end read data. Read file names should end with .fastq or .fq, with the optional addition of .gz. When possible, Theiagen recommends zipping files with gzip before Terra uploads to minimize data upload time.

By default, the workflow anticipates 2 x 150bp reads (i.e. the input reads were generated using a 300-cycle sequencing kit). Modifications to the optional parameter for trim_minlen may be required to accommodate shorter read data, such as the 2 x 75bp reads generated using a 150-cycle sequencing kit.

The TheiaEuk_ONT workflow takes in base-called ONT read data. Read file names should end with .fastq or .fq, with the optional addition of .gz. When possible, Theiagen recommends zipping files with gzip before uploading to Terra to minimize data upload time.

The ONT sequencing kit and base-calling approach can produce substantial variability in the amount and quality of read data. Genome assemblies produced by the TheiaEuk_ONT workflow must be quality assessed before reporting results.

Terra Task Name Variable Type Description Default Value Terra Status
theiaeuk_illumina_pe read1 File FASTQ file containing read1 sequences Required
theiaeuk_illumina_pe read2 File FASTQ file containing read2 sequences Required
theiaeuk_illumina_pe samplename String Sample name for the analysis Required
busco cpu Int Number of CPUs to allocate to the task 2 Optional
busco disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
cg_pipeline_clean cg_pipe_opts String Options to pass to CG-Pipeline for clean read assessment --fast Optional
cg_pipeline_clean disk_size Int Amount of storage (in GB) to allocate to the task 50 Optional
cg_pipeline_clean docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/lyveset:1.1.4f Optional
cg_pipeline_raw cg_pipe_opts String Options to pass to CG-Pipeline for raw read assessment --fast Optional
cg_pipeline_raw disk_size Int Amount of storage (in GB) to allocate to the task 50 Optional
cg_pipeline_raw docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/lyveset:1.1.4f Optional
clean_check_reads cpu Int Number of CPUs to allocate to the task 1 Optional
clean_check_reads disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
clean_check_reads docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/bactopia/gather_samples:2.0.2 Optional
clean_check_reads memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
digger_denovo assembler String Assembler to use (spades, skesa, megahit) skesa Optional
digger_denovo assembler_options String Assembler-specific options that you might choose for the selected assembler Optional
digger_denovo bwa_cpu Int Number of CPUs to allocate to the task 6 Optional
digger_denovo bwa_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
digger_denovo bwa_docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan Optional
digger_denovo bwa_memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
digger_denovo call_pilon Boolean Whether to run Pilon polishing after assembly FALSE Optional
digger_denovo filter_contigs_cpu Int Number of CPUs to allocate to the task 1 Optional
digger_denovo filter_contigs_disk_size Int Amount of storage (in GB) to allocate to the task 50 Optional
digger_denovo filter_contigs_docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/shovilter:0.2 Optional
digger_denovo filter_contigs_memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
digger_denovo filter_contigs_min_coverage Float Minimum coverage threshold for contig filtering 2.0 Optional
digger_denovo filter_contigs_skip_coverage_filter Boolean Skip filtering contigs based on coverage FALSE Optional
digger_denovo filter_contigs_skip_homopolymer_filter Boolean Skip filtering contigs containing homopolymers FALSE Optional
digger_denovo filter_contigs_skip_length_filter Boolean Skip filtering contigs based on length FALSE Optional
digger_denovo kmers String K-mer sizes for assembly (comma-separated) Optional
digger_denovo megahit_cpu Int Number of CPUs to allocate to the task 4 Optional
digger_denovo megahit_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
digger_denovo megahit_docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/megahit:1.2.9 Optional
digger_denovo megahit_memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
digger_denovo pilon_cpu Int Number of CPUs to allocate to the task 8 Optional
digger_denovo pilon_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
digger_denovo pilon_docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/biocontainers/pilon:1.24--hdfd78af_0 Optional
digger_denovo pilon_fix String Potential issues with assembly to try and automatically fix (snps, indels, gaps, local, all, bases, none) bases Optional
digger_denovo pilon_memory Int Amount of memory/RAM (in GB) to allocate to the task 32 Optional
digger_denovo pilon_min_base_quality Int Minimum base quality to keep 3 Optional
digger_denovo pilon_min_depth Float Minimum coverage threshold for variant calling: when set to a value ≥1, it requires that absolute depth of coverage; when set to a fraction <1, it requires coverage at least that fraction of the mean coverage for the region 0.25 Optional
digger_denovo pilon_min_mapping_quality Int Minimum mapping quality for a read to count in pileups 60 Optional
digger_denovo run_filter_contigs Boolean Whether to run contig filtering step TRUE Optional
digger_denovo skesa_cpu Int Number of CPUs to allocate to the task 4 Optional
digger_denovo skesa_disk_size Int Amount of storage (in GB) to allocate to the task 50 Optional
digger_denovo skesa_docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/skesa:2.4.0 Optional
digger_denovo skesa_memory Int Amount of memory/RAM (in GB) to allocate to the task 4 Optional
digger_denovo spades_cpu Int Number of CPUs to allocate to the task 16 Optional
digger_denovo spades_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
digger_denovo spades_docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/spades:4.1.0 Optional
digger_denovo spades_memory Int Amount of memory/RAM (in GB) to allocate to the task 32 Optional
digger_denovo spades_type String SPAdes assembly mode (isolate, meta, rna, etc.), more can be found here isolate Optional
gambit disk_size Int Amount of storage (in GB) to allocate to the task 20 Optional
gambit docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0 Optional
merlin_magic abricate_abaum_docker_image String Internal component, do not modify Optional
merlin_magic abricate_abaum_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic abricate_abaum_min_percent_identity Int Internal component, do not modify 95 Optional
merlin_magic abricate_vibrio_docker_image String Internal component, do not modify Optional
merlin_magic abricate_vibrio_min_percent_coverage Int Internal component, do not modify 80 Optional
merlin_magic abricate_vibrio_min_percent_identity Int Internal component, do not modify 80 Optional
merlin_magic agrvate_agr_typing_only Boolean Internal component, do not modify Optional
merlin_magic agrvate_docker_image String Internal component, do not modify Optional
merlin_magic amr_search_cpu Int Number of CPUs to allocate to the task 2 Optional
merlin_magic amr_search_disk_size Int Amount of storage (in GB) to allocate to the task 50 Optional
merlin_magic amr_search_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.1 Optional
merlin_magic amr_search_memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
merlin_magic assembly_only Boolean Set to true if only analyzing input assembly FALSE Optional
merlin_magic call_poppunk Boolean Internal component, do not modify TRUE Optional
merlin_magic call_shigeifinder_reads_input Boolean Internal component, do not modify FALSE Optional
merlin_magic call_stxtyper Boolean Internal component, do not modify FALSE Optional
merlin_magic call_tbp_parser Boolean Internal component, do not modify FALSE Optional
merlin_magic cauris_cladetyper_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0 Optional
merlin_magic cladetyper_kmer_size Int Kmer size for cladtyper Optional
merlin_magic cladetyper_max_distance Float The maximum GAMBIT distance to report a C. auris clade hit 0.1 Optional
merlin_magic cladetyper_ref_clade1 File Reference genome FASTA for Candidozyma auris clade1 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.2_Cand_auris_B8441_V2_genomic.fasta Optional
merlin_magic cladetyper_ref_clade1_annotated File Reference GBFF annotation for C. auris clade1 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435_Cauris_B8441_V2_genomic.gbff Optional
merlin_magic cladetyper_ref_clade2 File Reference genome FASTA for C. auris clade2 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.fasta Optional
merlin_magic cladetyper_ref_clade2_annotated File Reference GBFF annotation for C. auris clade2 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.gbff Optional
merlin_magic cladetyper_ref_clade3 File Reference genome FASTA for C. auris clade3 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.fasta Optional
merlin_magic cladetyper_ref_clade3_annotated File Reference GBFF annotation for C. auris clade3 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.gbff Optional
merlin_magic cladetyper_ref_clade4 File Reference genome FASTA for C. auris clade4 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.fasta Optional
merlin_magic cladetyper_ref_clade4_annotated File Reference GBFF annotation for C. auris clade4 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.gbff Optional
merlin_magic cladetyper_ref_clade5 File Reference genome FASTA for C. auris clade5 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.fasta Optional
merlin_magic cladetyper_ref_clade5_annotated File Reference GBFF annotation for C. auris clade5 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.gbff Optional
merlin_magic cladetyper_ref_clade6 File Reference genome FASTA for C. auris clade6 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade6_GCA_032714025.1_ASM3271402v1_genomic.fasta Optional
merlin_magic cladetyper_ref_clade6_annotated File Reference GBFF annotation for C. auris clade6 Optional
merlin_magic clockwork_docker_image String Internal component, do not modify Optional
merlin_magic ectyper_docker_image String Internal component, do not modify Optional
merlin_magic ectyper_h_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic ectyper_h_min_percent_identity Int Internal component, do not modify Optional
merlin_magic ectyper_o_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic ectyper_o_min_percent_identity Int Internal component, do not modify Optional
merlin_magic ectyper_print_alleles Boolean Internal component, do not modify Optional
merlin_magic ectyper_verify Boolean Internal component, do not modify Optional
merlin_magic emmtyper_align_diff Int Internal component, do not modify Optional
merlin_magic emmtyper_cluster_distance Int Internal component, do not modify Optional
merlin_magic emmtyper_culling_limit Int Internal component, do not modify Optional
merlin_magic emmtyper_docker_image String Internal component, do not modify Optional
merlin_magic emmtyper_gap Int Internal component, do not modify Optional
merlin_magic emmtyper_max_size Int Internal component, do not modify Optional
merlin_magic emmtyper_min_good Int Internal component, do not modify Optional
merlin_magic emmtyper_min_percent_identity Int Internal component, do not modify Optional
merlin_magic emmtyper_min_perfect Int Internal component, do not modify Optional
merlin_magic emmtyper_mismatch Int Internal component, do not modify Optional
merlin_magic emmtyper_wf String Internal component, do not modify Optional
merlin_magic emmtypingtool_docker_image String Internal component, do not modify Optional
merlin_magic genotyphi_docker_image String Internal component, do not modify Optional
merlin_magic hicap_broken_gene_length Int Internal component, do not modify Optional
merlin_magic hicap_docker_image String Internal component, do not modify Optional
merlin_magic hicap_min_broken_gene_percent_identity Float Internal component, do not modify Optional
merlin_magic hicap_min_gene_percent_coverage Float Internal component, do not modify Optional
merlin_magic hicap_min_gene_percent_identity Float Internal component, do not modify Optional
merlin_magic kaptive_docker_image String Internal component, do not modify Optional
merlin_magic kaptive_low_gene_percent_identity Float Internal component, do not modify Optional
merlin_magic kaptive_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic kaptive_min_percent_identity Float Internal component, do not modify Optional
merlin_magic kaptive_start_end_margin Int Internal component, do not modify Optional
merlin_magic kleborate_docker_image String Internal component, do not modify Optional
merlin_magic kleborate_min_kaptive_confidence String Internal component, do not modify Optional
merlin_magic kleborate_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic kleborate_min_percent_identity Float Internal component, do not modify Optional
merlin_magic kleborate_min_spurious_percent_coverage Float Internal component, do not modify Optional
merlin_magic kleborate_min_spurious_percent_identity Float Internal component, do not modify Optional
merlin_magic kleborate_skip_kaptive Boolean Internal component, do not modify Optional
merlin_magic kleborate_skip_resistance Boolean Internal component, do not modify Optional
merlin_magic legsta_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/biocontainers/legsta:0.5.1--hdfd78af_2 Optional
merlin_magic lissero_docker_image String Internal component, do not modify Optional
merlin_magic lissero_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic lissero_min_percent_identity Float Internal component, do not modify Optional
merlin_magic meningotype_docker_image String Internal component, do not modify Optional
merlin_magic ngmaster_docker_image String Internal component, do not modify Optional
merlin_magic ont_data Boolean Set to true if your data is ONT FASTQ files FALSE Optional
merlin_magic paired_end Boolean Set to true if your data is paired-end FASTQ files TRUE Optional
merlin_magic pasty_docker_image String Internal component, do not modify Optional
merlin_magic pasty_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic pasty_min_percent_identity Int Internal component, do not modify Optional
merlin_magic pbptyper_docker_image String Internal component, do not modify Optional
merlin_magic pbptyper_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic pbptyper_min_percent_identity Int Internal component, do not modify Optional
merlin_magic poppunk_docker_image String Internal component, do not modify Optional
merlin_magic poppunk_gps_clusters_csv File Internal component, do not modify Optional
merlin_magic poppunk_gps_dists_npy File Internal component, do not modify Optional
merlin_magic poppunk_gps_dists_pkl File Internal component, do not modify Optional
merlin_magic poppunk_gps_external_clusters_csv File Internal component, do not modify Optional
merlin_magic poppunk_gps_fit_npz File Internal component, do not modify Optional
merlin_magic poppunk_gps_fit_pkl File Internal component, do not modify Optional
merlin_magic poppunk_gps_graph_gt File Internal component, do not modify Optional
merlin_magic poppunk_gps_h5 File Internal component, do not modify Optional
merlin_magic poppunk_gps_qcreport_txt File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs_dists_npy File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs_dists_pkl File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs_graph_gt File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs_h5 File Internal component, do not modify Optional
merlin_magic poppunk_gps_unword_clusters_csv File Internal component, do not modify Optional
merlin_magic run_amr_search Boolean If set to true AMR_Search workflow will be run if species is part of supported taxon, see AMR_Search docs. FALSE Optional
merlin_magic seqsero2_docker_image String Internal component, do not modify Optional
merlin_magic seroba_docker_image String Internal component, do not modify Optional
merlin_magic serotypefinder_docker_image String Internal component, do not modify Optional
merlin_magic shigatyper_docker_image String Internal component, do not modify Optional
merlin_magic shigeifinder_docker_image String Internal component, do not modify Optional
merlin_magic sistr_cpu Int Internal component, do not modify Optional
merlin_magic sistr_disk_size Int Internal component, do not modify Optional
merlin_magic sistr_docker_image String Internal component, do not modify Optional
merlin_magic sistr_memory Int Internal component, do not modify Optional
merlin_magic sistr_use_full_cgmlst_db Boolean Internal component, do not modify Optional
merlin_magic snippy_base_quality Int Minimum quality for a nucleotide to be used in variant calling 13 Optional
merlin_magic snippy_gene_query_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 Optional
merlin_magic snippy_map_qual Int Minimum mapping quality to accept in variant calling 60 Optional
merlin_magic snippy_maxsoft Int Number of bases of alignment to soft-clip before discarding the alignment 10 Optional
merlin_magic snippy_min_coverage Int Minimum read coverage of a position to identify a mutation 10 Optional
merlin_magic snippy_min_frac Float Minimum fraction of bases at a given position to identify a mutation 0 Optional
merlin_magic snippy_min_quality Int Minimum VCF variant call "quality" 100 Optional
merlin_magic snippy_query_gene String Provide a gene to search for using Snippy Default depend on detected organism Optional
merlin_magic snippy_reference_afumigatus File Snippy reference for Aspergillus fumigatus gs://theiagen-public-resources-rp/reference_data/eukaryotic/aspergillus/Aspergillus_fumigatus_GCF_000002655.1_ASM265v1_genomic.gbff Optional
merlin_magic snippy_reference_cryptoneo File Snippy reference for Cryptococcus neoformans gs://theiagen-public-resources-rp/reference_data/eukaryotic/cryptococcus/Cryptococcus_neoformans_GCF_000091045.1_ASM9104v1_genomic.gbff Optional
merlin_magic snippy_variants_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/snippy:4.6.0 Optional
merlin_magic sonneityping_docker_image String Internal component, do not modify Optional
merlin_magic sonneityping_mykrobe_opts String Internal component, do not modify Optional
merlin_magic spatyper_do_enrich Boolean Internal component, do not modify Optional
merlin_magic spatyper_docker_image String Internal component, do not modify Optional
merlin_magic srst2_docker_image String Internal component, do not modify Optional
merlin_magic srst2_gene_max_mismatch Int Internal component, do not modify 2000 Optional
merlin_magic srst2_max_divergence Int Internal component, do not modify 20 Optional
merlin_magic srst2_min_depth Int Internal component, do not modify 5 Optional
merlin_magic srst2_min_edge_depth Int Internal component, do not modify 2 Optional
merlin_magic srst2_min_percent_coverage Int Internal component, do not modify 80 Optional
merlin_magic staphopia_sccmec_docker_image String Internal component, do not modify Optional
merlin_magic stxtyper_cpu Int Internal component, do not modify Optional
merlin_magic stxtyper_disk_size Int Internal component, do not modify Optional
merlin_magic stxtyper_docker_image String Internal component, do not modify Optional
merlin_magic stxtyper_enable_debug Boolean Internal component, do not modify Optional
merlin_magic stxtyper_memory Int Internal component, do not modify Optional
merlin_magic tbp_parser_add_cs_lims Boolean Internal component, do not modify Optional
merlin_magic tbp_parser_config File Internal component, do not modify Optional
merlin_magic tbp_parser_coverage_regions_bed File Internal component, do not modify Optional
merlin_magic tbp_parser_debug Boolean Internal component, do not modify Optional
merlin_magic tbp_parser_docker_image String Internal component, do not modify Optional
merlin_magic tbp_parser_etha237_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_expert_rule_regions_bed File Internal component, do not modify Optional
merlin_magic tbp_parser_min_depth Int Internal component, do not modify Optional
merlin_magic tbp_parser_min_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic tbp_parser_min_read_support Int Internal component, do not modify Optional
merlin_magic tbp_parser_operator String Internal component, do not modify Optional
merlin_magic tbp_parser_output_seq_method_type String Internal component, do not modify WGS Optional
merlin_magic tbp_parser_rpob449_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_rrl_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_rrl_read_support Int Internal component, do not modify Optional
merlin_magic tbp_parser_rrs_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_rrs_read_support Int Internal component, do not modify Optional
merlin_magic tbp_parser_tngs_data Boolean Internal component, do not modify Optional
merlin_magic tbprofiler_additional_parameters String Internal component, do not modify Optional
merlin_magic tbprofiler_custom_db File Internal component, do not modify Optional
merlin_magic tbprofiler_docker_image String Internal component, do not modify Optional
merlin_magic tbprofiler_mapper String Internal component, do not modify Optional
merlin_magic tbprofiler_min_af Float Internal component, do not modify Optional
merlin_magic tbprofiler_min_depth Int Internal component, do not modify Optional
merlin_magic tbprofiler_run_cdph_db Boolean Internal component, do not modify FALSE Optional
merlin_magic tbprofiler_run_custom_db Boolean Internal component, do not modify FALSE Optional
merlin_magic tbprofiler_variant_caller String Internal component, do not modify Optional
merlin_magic tbprofiler_variant_calling_params String Internal component, do not modify Optional
merlin_magic vibecheck_docker_image String Internal component, do not modify Optional
merlin_magic vibecheck_lineage_barcodes File Internal component, do not modify Optional
merlin_magic vibecheck_skip_subsampling Boolean Internal component, do not modify Optional
merlin_magic vibecheck_subsampling_fraction Float Internal component, do not modify Optional
merlin_magic virulencefinder_database String Internal component, do not modify Optional
merlin_magic virulencefinder_docker_image String Internal component, do not modify Optional
merlin_magic virulencefinder_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic virulencefinder_min_percent_identity Float Internal component, do not modify Optional
qc_check_task ani_highest_percent Float Internal component, do not modify Optional
qc_check_task ani_highest_percent_bases_aligned Float Internal component, do not modify Optional
qc_check_task assembly_length_unambiguous Int Internal component, do not modify Optional
qc_check_task assembly_mean_coverage Float Internal component, do not modify Optional
qc_check_task cpu Int Number of CPUs to allocate to the task 4 Optional
qc_check_task disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
qc_check_task docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16 Optional
qc_check_task kraken_human Float Internal component, do not modify Optional
qc_check_task kraken_human_dehosted Float Internal component, do not modify Optional
qc_check_task kraken_sc2 Float Internal component, do not modify Optional
qc_check_task kraken_sc2_dehosted Float Internal component, do not modify Optional
qc_check_task kraken_target_organism Float Internal component, do not modify Optional
qc_check_task kraken_target_organism_dehosted Float Internal component, do not modify Optional
qc_check_task meanbaseq_trim String Internal component, do not modify Optional
qc_check_task memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
qc_check_task midas_secondary_genus_abundance Float Internal component, do not modify Optional
qc_check_task midas_secondary_genus_coverage Float Internal component, do not modify Optional
qc_check_task number_Degenerate Int Internal component, do not modify Optional
qc_check_task number_N Int Internal component, do not modify Optional
qc_check_task percent_reference_coverage Float Internal component, do not modify Optional
qc_check_task sc2_s_gene_mean_coverage Float Internal component, do not modify Optional
qc_check_task sc2_s_gene_percent_coverage Float Internal component, do not modify Optional
qc_check_task vadr_num_alerts String Internal component, do not modify Optional
quast disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
quast docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/quast:5.0.2 Optional
quast min_contig_length Int Minimum length of contig for QUAST 500 Optional
rasusa_task bases String Explicitly set the number of bases required e.g., 4.3kb, 7Tb, 9000, 4.1MB. If this option is given, --coverage and --genome-size are ignored Optional
rasusa_task cpu Int Number of CPUs to allocate to the task 4 Optional
rasusa_task disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
rasusa_task docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0 Optional
rasusa_task frac Float Explicitly define the fraction of reads to keep in the subsample; when used, genome size and coverage are ignored; acceptable inputs include whole numbers and decimals, e.g. 50.0 will leave 50% of the reads in the subsample Optional
rasusa_task memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
rasusa_task num Int Optional: explicitly define the number of reads in the subsample; when used, genome size and coverage are ignored; acceptable metric suffixes include: b, k, m, g, and t for base, kilo, mega, giga, and tera, respectively Optional
rasusa_task seed Int Use to assign a name to the "random seed" that is used by the subsampler; i.e. this allows the exact same subsample to be produced from the same input file/s in subsequent runs when providing the seed identifier; do not input values for random downsampling Optional
raw_check_reads cpu Int Number of CPUs to allocate to the task 1 Optional
raw_check_reads disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
raw_check_reads docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/bactopia/gather_samples:2.0.2 Optional
raw_check_reads memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
read_QC_trim adapters File File with adapter sequences to be removed Optional
read_QC_trim bbduk_memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
read_QC_trim call_kraken Boolean True/False variable that determines if the Kraken2 task should be called; for non-TheiaCoV workflows, the kraken_db variable must be provided. FALSE Optional
read_QC_trim call_midas Boolean Internal component, do not modify FALSE Optional
read_QC_trim extract_unclassified Boolean Internal component, do not modify FALSE Optional
read_QC_trim fastp_args String Additional arguments to use with fastp --detect_adapter_for_pe -g -5 20 -3 20 Optional
read_QC_trim host String Internal component, do not modify Optional
read_QC_trim host_complete_only Boolean Internal component, do not modify FALSE Optional
read_QC_trim host_decontaminate_mem Int Internal component, do not modify 32 Optional
read_QC_trim host_is_accession Boolean Internal component, do not modify FALSE Optional
read_QC_trim host_refseq Boolean Internal component, do not modify TRUE Optional
read_QC_trim kraken_cpu Int Number of CPUs to allocate to the task 4 Optional
read_QC_trim kraken_db File A kraken2 database to use with the kraken2 optional task. The file must be a .tar.gz kraken2 database. Optional
read_QC_trim kraken_disk_size Int Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database) 100 Optional
read_QC_trim kraken_memory Int Amount of memory/RAM (in GB) to allocate to the task 32 Optional
read_QC_trim midas_db File Internal component, do not modify gs://theiagen-public-files-rp/terra/theiaprok-files/midas/midas_db_v1.2.tar.gz Optional
read_QC_trim phix File A file containing the phix used during Illumina sequencing; used in the BBDuk task Optional
read_QC_trim read_processing String The name of the tool to perform basic read processing; options: "trimmomatic" or "fastp" trimmomatic Optional
read_QC_trim read_qc String The tool used for quality control (QC) of reads. Options are "fastq_scan" (default) and "fastqc" fastq_scan Optional
read_QC_trim target_organism String This string is searched for in the kraken2 outputs to extract the read percentage Optional
read_QC_trim taxon_id Int Internal component, do not modify 0 Optional
read_QC_trim trimmomatic_args String Additional arguments to pass to trimmomatic. "-phred33" specifies the Phred Q score encoding which is almost always phred33 with modern sequence data. -phred33 Optional
read_QC_trim workflow_series String Internal component, do not modify Optional
theiaeuk_illumina_pe busco_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.3.2_cv1 Optional
theiaeuk_illumina_pe busco_memory Int Amount of memory/RAM (in GB) to allocate to the task 24 Optional
theiaeuk_illumina_pe call_rasusa Boolean If true, RASUSA will subsample raw reads to a specified read depth (150X by default) TRUE Optional
theiaeuk_illumina_pe cpu Int Number of CPUs to allocate to the task 8 Optional
theiaeuk_illumina_pe expected_taxon String If provided, this input will override the taxonomic assignment made by GAMBIT and launch the relevant taxon-specific submodules. It will also modify the organism flag used by AMRFinderPlus. Example format: "Salmonella enterica" Optional
theiaeuk_illumina_pe gambit_db_genomes File User-provided database of assembled query genomes; requires complementary signatures file. If not provided, uses default database, "/gambit-db" gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-metadata-1.0.0-20241213.gdb Optional
theiaeuk_illumina_pe gambit_db_signatures File User-provided signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used. gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-signatures-1.0.0-20241213.gs Optional
theiaeuk_illumina_pe genome_length Int User-specified expected genome length to be used in genome statistics calculations Optional
theiaeuk_illumina_pe max_genome_length Int Maximum genome size able to pass read screening 178000000 Optional
theiaeuk_illumina_pe memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
theiaeuk_illumina_pe min_basepairs Int Minimum number of base pairs able to pass read screening 45000000 Optional
theiaeuk_illumina_pe min_contig_length Int Minimum contig length for assembler 1000 Optional
theiaeuk_illumina_pe min_coverage Int Minimum genome coverage able to pass read screening 10 Optional
theiaeuk_illumina_pe min_genome_length Int Minimum genome size able to pass read screening 9000000 Optional
theiaeuk_illumina_pe min_proportion Int Minimum proportion of total reads in each read file to pass read screening 40 Optional
theiaeuk_illumina_pe min_reads Int Minimum number of reads to pass read screening 30000 Optional
theiaeuk_illumina_pe qc_check_table File TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table. Optional
theiaeuk_illumina_pe seq_method String Sequencing method used for the samples ILLUMINA Optional
theiaeuk_illumina_pe skip_screen Boolean Option to skip the read screening prior to analysis; if setting to true, please provide a value for the theiaeuk_pe genome_length optional input, OR set call_rasusa to false. Otherwise RASUSA will attempt to downsample to an expected genome size of 0 bp, and the workflow will fail. FALSE Optional
theiaeuk_illumina_pe subsample_coverage Float Read depth for RASUSA task to subsample reads to 150 Optional
theiaeuk_illumina_pe trim_min_length Int Specifies minimum length of each read after trimming to be kept 75 Optional
theiaeuk_illumina_pe trim_quality_min_score Int Specifies the minimum average quality of bases in a sliding window to be kept 20 Optional
theiaeuk_illumina_pe trim_window_size Int Size of the trimming window to use 10 Optional
version_capture docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0 Optional
version_capture timezone String Set the time zone to get an accurate date of analysis (uses UTC by default) Optional
Terra Task Name Variable Type Description Default Value Terra Status
theiaeuk_ont read1 File ONT read file in FASTQ file format (compression optional) Required
theiaeuk_ont samplename String The name of the sample being analyzed Required
busco cpu Int Number of CPUs to allocate to the task 2 Optional
busco disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
clean_check_reads cpu Int Number of CPUs to allocate to the task 1 Optional
clean_check_reads disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
clean_check_reads docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/bactopia/gather_samples:2.0.2 Optional
clean_check_reads memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
clean_check_reads workflow_series String Internal component, do not modify theiaviral Optional
flye_denovo auto_medaka_model Boolean If true, medaka will automatically select the best Medaka model for assembly TRUE Optional
flye_denovo bandage_cpu Int Number of CPUs to allocate to the task 2 Optional
flye_denovo bandage_disk_size Int Amount of storage (in GB) to allocate to the task 10 Optional
flye_denovo bandage_memory Int Amount of memory/RAM (in GB) to allocate to the task 4 Optional
flye_denovo dnaapler_cpu Int Number of CPUs to allocate to the task 1 Optional
flye_denovo dnaapler_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
flye_denovo dnaapler_memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
flye_denovo dnaapler_mode String Dnaapler-specific inputs all Optional
flye_denovo filter_contigs_cpu Int Number of CPUs to allocate to the task 1 Optional
flye_denovo filter_contigs_disk_size Int Amount of storage (in GB) to allocate to the task 10 Optional
flye_denovo filter_contigs_memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
flye_denovo filter_contigs_min_length Int Minimum contig length to keep 1000 Optional
flye_denovo flye_additional_parameters String Any extra Flye-specific parameters Optional
flye_denovo flye_asm_coverage Int Reduced coverage for initial disjointig assembly Optional
flye_denovo flye_cpu Int Number of CPUs to allocate to the task 4 Optional
flye_denovo flye_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
flye_denovo flye_genome_length Int User-specified expected genome length to be used in genome statistics calculations Optional
flye_denovo flye_keep_haplotypes Boolean If true keep haplotypes FALSE Optional
flye_denovo flye_memory Int Amount of memory/RAM (in GB) to allocate to the task 32 Optional
flye_denovo flye_minimum_overlap Int Minimum overlap between reads Optional
flye_denovo flye_no_alt_contigs Boolean If true, do not generate alternative contigs FALSE Optional
flye_denovo flye_polishing_iterations Int Default polishing iterations 1 Optional
flye_denovo flye_read_error_rate Float Maximum expected read error rate Optional
flye_denovo flye_read_type String Specifies the type of sequencing reads. Options: --nano-hq (default), --nano-corr, --nano-raw, --pacbio-raw, --pacbio-corr, --pacbio-hifi. Refer to Flye documentation for details on each type. --nano-hq Optional
flye_denovo flye_scaffold Boolean If true, scaffolding is enabled using graph FALSE Optional
flye_denovo flye_uneven_coverage_mode Boolean sets the --meta option in the case of uneven coverage (or metagenomics) FALSE Optional
flye_denovo illumina_read1 File If Illumina reads are provided, flye_denovo subworkflow will perform Illumina polishing Optional
flye_denovo illumina_read2 File If Illumina reads are provided, flye_denovo subworkflow will perform Illumina polishing Optional
flye_denovo medaka_cpu Int Number of CPUs to allocate to the task 4 Optional
flye_denovo medaka_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
flye_denovo medaka_memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
flye_denovo medaka_model String In order to obtain the best results, the appropriate model must be set to match the sequencer's basecaller model; this string takes the format of {pore}{device}{caller variant}_{caller_version}. See also https://github.com/nanoporetech/medaka?tab=readme-ov-file#models. If this is being run on legacy data it is likely to be r941_min_hac_g507. r1041_e82_400bps_sup_v5.0.0 Optional
flye_denovo polish_rounds Int The number of polishing rounds to conduct for medaka or racon (without Illumina) 1 Optional
flye_denovo polisher String The polishing tool to use for assembly medaka Optional
flye_denovo polypolish_careful Boolean Polypolish-specific inputs FALSE Optional
flye_denovo polypolish_cpu Int Number of CPUs to allocate to the task 1 Optional
flye_denovo polypolish_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
flye_denovo polypolish_fraction_invalid Float Polypolish-specific inputs Optional
flye_denovo polypolish_fraction_valid Float Polypolish-specific inputs Optional
flye_denovo polypolish_high_percentile_threshold Float Polypolish-specific inputs Optional
flye_denovo polypolish_low_percentile_threshold Float Polypolish-specific inputs Optional
flye_denovo polypolish_maximum_errors Int Polypolish-specific inputs Optional
flye_denovo polypolish_memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
flye_denovo polypolish_minimum_depth Int Polypolish-specific inputs Optional
flye_denovo polypolish_pair_orientation String Polypolish-specific inputs Optional
flye_denovo porechop_cpu Int Number of CPUs to allocate to the task 4 Optional
flye_denovo porechop_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
flye_denovo porechop_memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
flye_denovo porechop_trimopts String Options to pass to Porechop for trimming Optional
flye_denovo racon_cpu Int Number of CPUs to allocate to the task 8 Optional
flye_denovo racon_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
flye_denovo racon_memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
flye_denovo run_porechop Boolean If true, trims reads before assembly using Porechop FALSE Optional
flye_denovo skip_polishing Boolean If true, skips polishing FALSE Optional
gambit cpu Int Number of CPUs to allocate to the task 1 Optional
gambit disk_size Int Amount of storage (in GB) to allocate to the task 20 Optional
gambit docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0 Optional
gambit memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
merlin_magic abricate_abaum_docker_image String Internal component, do not modify Optional
merlin_magic abricate_abaum_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic abricate_abaum_min_percent_identity Int Internal component, do not modify 95 Optional
merlin_magic abricate_vibrio_docker_image String Internal component, do not modify Optional
merlin_magic abricate_vibrio_min_percent_coverage Int Internal component, do not modify 80 Optional
merlin_magic abricate_vibrio_min_percent_identity Int Internal component, do not modify 80 Optional
merlin_magic agrvate_agr_typing_only Boolean Internal component, do not modify Optional
merlin_magic agrvate_docker_image String Internal component, do not modify Optional
merlin_magic agrvate_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/biocontainers/agrvate:1.0.2--hdfd78af_0 Optional
merlin_magic amr_search_cpu Int Number of CPUs to allocate to the task 2 Optional
merlin_magic amr_search_disk_size Int Amount of storage (in GB) to allocate to the task 50 Optional
merlin_magic amr_search_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.1 Optional
merlin_magic amr_search_memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
merlin_magic call_poppunk Boolean Internal component, do not modify TRUE Optional
merlin_magic call_shigeifinder_reads_input Boolean Internal component, do not modify FALSE Optional
merlin_magic call_stxtyper Boolean Internal component, do not modify FALSE Optional
merlin_magic call_tbp_parser Boolean Internal component, do not modify FALSE Optional
merlin_magic cauris_cladetyper_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0 Optional
merlin_magic cladetyper_kmer_size Int Kmer size for cladtyper Optional
merlin_magic cladetyper_max_distance Float The maximum GAMBIT distance to report a C. auris clade hit 0.1 Optional
merlin_magic cladetyper_ref_clade1 File Reference genome FASTA for Candidozyma auris clade1 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.2_Cand_auris_B8441_V2_genomic.fasta Optional
merlin_magic cladetyper_ref_clade1_annotated File Reference GBFF annotation for C. auris clade1 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435_Cauris_B8441_V2_genomic.gbff Optional
merlin_magic cladetyper_ref_clade2 File Reference genome FASTA for C. auris clade2 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.fasta Optional
merlin_magic cladetyper_ref_clade2_annotated File Reference GBFF annotation for C. auris clade2 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.gbff Optional
merlin_magic cladetyper_ref_clade3 File Reference genome FASTA for C. auris clade3 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.fasta Optional
merlin_magic cladetyper_ref_clade3_annotated File Reference GBFF annotation for C. auris clade3 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.gbff Optional
merlin_magic cladetyper_ref_clade4 File Reference genome FASTA for C. auris clade4 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.fasta Optional
merlin_magic cladetyper_ref_clade4_annotated File Reference GBFF annotation for C. auris clade4 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.gbff Optional
merlin_magic cladetyper_ref_clade5 File Reference genome FASTA for C. auris clade5 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.fasta Optional
merlin_magic cladetyper_ref_clade5_annotated File Reference GBFF annotation for C. auris clade5 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.gbff Optional
merlin_magic cladetyper_ref_clade6 File Reference genome FASTA for C. auris clade6 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade6_GCA_032714025.1_ASM3271402v1_genomic.fasta Optional
merlin_magic cladetyper_ref_clade6_annotated File Reference GBFF annotation for C. auris clade6 Optional
merlin_magic clockwork_docker_image String Internal component, do not modify Optional
merlin_magic ectyper_docker_image String Internal component, do not modify Optional
merlin_magic ectyper_h_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic ectyper_h_min_percent_identity Int Internal component, do not modify Optional
merlin_magic ectyper_o_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic ectyper_o_min_percent_identity Int Internal component, do not modify Optional
merlin_magic ectyper_print_alleles Boolean Internal component, do not modify Optional
merlin_magic ectyper_verify Boolean Internal component, do not modify Optional
merlin_magic emmtyper_align_diff Int Internal component, do not modify Optional
merlin_magic emmtyper_cluster_distance Int Internal component, do not modify Optional
merlin_magic emmtyper_culling_limit Int Internal component, do not modify Optional
merlin_magic emmtyper_docker_image String Internal component, do not modify Optional
merlin_magic emmtyper_gap Int Internal component, do not modify Optional
merlin_magic emmtyper_max_size Int Internal component, do not modify Optional
merlin_magic emmtyper_min_good Int Internal component, do not modify Optional
merlin_magic emmtyper_min_percent_identity Int Internal component, do not modify Optional
merlin_magic emmtyper_min_perfect Int Internal component, do not modify Optional
merlin_magic emmtyper_mismatch Int Internal component, do not modify Optional
merlin_magic emmtyper_wf String Internal component, do not modify Optional
merlin_magic emmtypingtool_docker_image String Internal component, do not modify Optional
merlin_magic genotyphi_docker_image String Internal component, do not modify Optional
merlin_magic hicap_broken_gene_length Int Internal component, do not modify Optional
merlin_magic hicap_docker_image String Internal component, do not modify Optional
merlin_magic hicap_min_broken_gene_percent_identity Float Internal component, do not modify Optional
merlin_magic hicap_min_gene_percent_coverage Float Internal component, do not modify Optional
merlin_magic hicap_min_gene_percent_identity Float Internal component, do not modify Optional
merlin_magic kaptive_docker_image String Internal component, do not modify Optional
merlin_magic kaptive_low_gene_percent_identity Float Internal component, do not modify Optional
merlin_magic kaptive_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic kaptive_min_percent_identity Float Internal component, do not modify Optional
merlin_magic kaptive_start_end_margin Int Internal component, do not modify Optional
merlin_magic kleborate_docker_image String Internal component, do not modify Optional
merlin_magic kleborate_min_kaptive_confidence String Internal component, do not modify Optional
merlin_magic kleborate_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic kleborate_min_percent_identity Float Internal component, do not modify Optional
merlin_magic kleborate_min_spurious_percent_coverage Float Internal component, do not modify Optional
merlin_magic kleborate_min_spurious_percent_identity Float Internal component, do not modify Optional
merlin_magic kleborate_skip_kaptive Boolean Internal component, do not modify Optional
merlin_magic kleborate_skip_resistance Boolean Internal component, do not modify Optional
merlin_magic legsta_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/biocontainers/legsta:0.5.1--hdfd78af_2 Optional
merlin_magic lissero_docker_image String Internal component, do not modify Optional
merlin_magic lissero_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic lissero_min_percent_identity Float Internal component, do not modify Optional
merlin_magic meningotype_docker_image String Internal component, do not modify Optional
merlin_magic ngmaster_docker_image String Internal component, do not modify Optional
merlin_magic paired_end Boolean Set to true if your data is paired-end FASTQ files TRUE Optional
merlin_magic pasty_docker_image String Internal component, do not modify Optional
merlin_magic pasty_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic pasty_min_percent_identity Int Internal component, do not modify Optional
merlin_magic pbptyper_docker_image String Internal component, do not modify Optional
merlin_magic pbptyper_min_percent_coverage Int Internal component, do not modify Optional
merlin_magic pbptyper_min_percent_identity Int Internal component, do not modify Optional
merlin_magic poppunk_docker_image String Internal component, do not modify Optional
merlin_magic poppunk_gps_clusters_csv File Internal component, do not modify Optional
merlin_magic poppunk_gps_dists_npy File Internal component, do not modify Optional
merlin_magic poppunk_gps_dists_pkl File Internal component, do not modify Optional
merlin_magic poppunk_gps_external_clusters_csv File Internal component, do not modify Optional
merlin_magic poppunk_gps_fit_npz File Internal component, do not modify Optional
merlin_magic poppunk_gps_fit_pkl File Internal component, do not modify Optional
merlin_magic poppunk_gps_graph_gt File Internal component, do not modify Optional
merlin_magic poppunk_gps_h5 File Internal component, do not modify Optional
merlin_magic poppunk_gps_qcreport_txt File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs_dists_npy File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs_dists_pkl File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs_graph_gt File Internal component, do not modify Optional
merlin_magic poppunk_gps_refs_h5 File Internal component, do not modify Optional
merlin_magic poppunk_gps_unword_clusters_csv File Internal component, do not modify Optional
merlin_magic read1 File Internal component, do not modify Optional
merlin_magic read2 File Internal component, do not modify Optional
merlin_magic run_amr_search Boolean If set to true AMR_Search workflow will be run if species is part of supported taxon, see AMR_Search docs. FALSE Optional
merlin_magic seqsero2_docker_image String Internal component, do not modify Optional
merlin_magic seroba_docker_image String Internal component, do not modify Optional
merlin_magic serotypefinder_docker_image String Internal component, do not modify Optional
merlin_magic shigatyper_docker_image String Internal component, do not modify Optional
merlin_magic shigeifinder_docker_image String Internal component, do not modify Optional
merlin_magic sistr_cpu Int Internal component, do not modify Optional
merlin_magic sistr_disk_size Int Internal component, do not modify Optional
merlin_magic sistr_docker_image String Internal component, do not modify Optional
merlin_magic sistr_memory Int Internal component, do not modify Optional
merlin_magic sistr_use_full_cgmlst_db Boolean Internal component, do not modify Optional
merlin_magic snippy_base_quality Int Minimum quality for a nucleotide to be used in variant calling 13 Optional
merlin_magic snippy_gene_query_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 Optional
merlin_magic snippy_map_qual Int Minimum mapping quality to accept in variant calling 60 Optional
merlin_magic snippy_maxsoft Int Number of bases of alignment to soft-clip before discarding the alignment 10 Optional
merlin_magic snippy_min_coverage Int Minimum read coverage of a position to identify a mutation 10 Optional
merlin_magic snippy_min_frac Float Minimum fraction of bases at a given position to identify a mutation 0 Optional
merlin_magic snippy_min_quality Int Minimum VCF variant call "quality" 100 Optional
merlin_magic snippy_query_gene String Provide a gene to search for using Snippy Default depend on detected organism Optional
merlin_magic snippy_reference_afumigatus File Snippy reference for Aspergillus fumigatus gs://theiagen-public-resources-rp/reference_data/eukaryotic/aspergillus/Aspergillus_fumigatus_GCF_000002655.1_ASM265v1_genomic.gbff Optional
merlin_magic snippy_reference_cryptoneo File Snippy reference for Cryptococcus neoformans gs://theiagen-public-resources-rp/reference_data/eukaryotic/cryptococcus/Cryptococcus_neoformans_GCF_000091045.1_ASM9104v1_genomic.gbff Optional
merlin_magic snippy_variants_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/snippy:4.6.0 Optional
merlin_magic sonneityping_docker_image String Internal component, do not modify Optional
merlin_magic sonneityping_mykrobe_opts String Internal component, do not modify Optional
merlin_magic spatyper_do_enrich Boolean Internal component, do not modify Optional
merlin_magic spatyper_docker_image String Internal component, do not modify Optional
merlin_magic srst2_docker_image String Internal component, do not modify Optional
merlin_magic srst2_gene_max_mismatch Int Internal component, do not modify 2000 Optional
merlin_magic srst2_max_divergence Int Internal component, do not modify 20 Optional
merlin_magic srst2_min_depth Int Internal component, do not modify 5 Optional
merlin_magic srst2_min_edge_depth Int Internal component, do not modify 2 Optional
merlin_magic srst2_min_percent_coverage Int Internal component, do not modify 80 Optional
merlin_magic staphopia_sccmec_docker_image String Internal component, do not modify Optional
merlin_magic stxtyper_cpu Int Internal component, do not modify Optional
merlin_magic stxtyper_disk_size Int Internal component, do not modify Optional
merlin_magic stxtyper_docker_image String Internal component, do not modify Optional
merlin_magic stxtyper_enable_debug Boolean Internal component, do not modify Optional
merlin_magic stxtyper_memory Int Internal component, do not modify Optional
merlin_magic tbp_parser_add_cs_lims Boolean Internal component, do not modify Optional
merlin_magic tbp_parser_config File Internal component, do not modify Optional
merlin_magic tbp_parser_coverage_regions_bed File Internal component, do not modify Optional
merlin_magic tbp_parser_debug Boolean Internal component, do not modify Optional
merlin_magic tbp_parser_docker_image String Internal component, do not modify Optional
merlin_magic tbp_parser_etha237_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_expert_rule_regions_bed File Internal component, do not modify Optional
merlin_magic tbp_parser_min_depth Int Internal component, do not modify Optional
merlin_magic tbp_parser_min_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic tbp_parser_min_read_support Int Internal component, do not modify Optional
merlin_magic tbp_parser_operator String Internal component, do not modify Optional
merlin_magic tbp_parser_output_seq_method_type String Internal component, do not modify WGS Optional
merlin_magic tbp_parser_rpob449_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_rrl_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_rrl_read_support Int Internal component, do not modify Optional
merlin_magic tbp_parser_rrs_frequency Float Internal component, do not modify Optional
merlin_magic tbp_parser_rrs_read_support Int Internal component, do not modify Optional
merlin_magic tbp_parser_tngs_data Boolean Internal component, do not modify Optional
merlin_magic tbprofiler_additional_parameters String Internal component, do not modify Optional
merlin_magic tbprofiler_custom_db File Internal component, do not modify Optional
merlin_magic tbprofiler_docker_image String Internal component, do not modify Optional
merlin_magic tbprofiler_mapper String Internal component, do not modify Optional
merlin_magic tbprofiler_min_af Float Internal component, do not modify Optional
merlin_magic tbprofiler_min_depth Int Internal component, do not modify Optional
merlin_magic tbprofiler_run_cdph_db Boolean Internal component, do not modify FALSE Optional
merlin_magic tbprofiler_run_custom_db Boolean Internal component, do not modify FALSE Optional
merlin_magic tbprofiler_variant_caller String Internal component, do not modify Optional
merlin_magic tbprofiler_variant_calling_params String Internal component, do not modify Optional
merlin_magic vibecheck_docker_image String Internal component, do not modify Optional
merlin_magic vibecheck_lineage_barcodes File Internal component, do not modify Optional
merlin_magic vibecheck_skip_subsampling Boolean Internal component, do not modify Optional
merlin_magic vibecheck_subsampling_fraction Float Internal component, do not modify Optional
merlin_magic virulencefinder_database String Internal component, do not modify Optional
merlin_magic virulencefinder_docker_image String Internal component, do not modify Optional
merlin_magic virulencefinder_min_percent_coverage Float Internal component, do not modify Optional
merlin_magic virulencefinder_min_percent_identity Float Internal component, do not modify Optional
nanoplot_clean cpu Int Number of CPUs to allocate to the task 4 Optional
nanoplot_clean disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
nanoplot_clean docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/nanoplot:1.40.0 Optional
nanoplot_clean max_length Int The maximum length of clean reads, for which reads longer than the length specified will be hidden. 100000 Optional
nanoplot_clean memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
nanoplot_raw cpu Int Number of CPUs to allocate to the task 4 Optional
nanoplot_raw disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
nanoplot_raw docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/nanoplot:1.40.0 Optional
nanoplot_raw max_length Int The maximum length of clean reads, for which reads longer than the length specified will be hidden. 100000 Optional
nanoplot_raw memory Int Amount of memory/RAM (in GB) to allocate to the task 16 Optional
quast cpu Int Number of CPUs to allocate to the task 2 Optional
quast disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
quast docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/quast:5.0.2 Optional
quast memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
quast min_contig_length Int Minimum length of contig for QUAST 500 Optional
raw_check_reads cpu Int Number of CPUs to allocate to the task 1 Optional
raw_check_reads disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
raw_check_reads docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/bactopia/gather_samples:2.0.2 Optional
raw_check_reads memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
raw_check_reads workflow_series String Internal component, do not modify theiaviral Optional
read_QC_trim artic_guppyplex_cpu Int Internal component, do not modify Optional
read_QC_trim artic_guppyplex_disk_size Int Internal component, do not modify Optional
read_QC_trim artic_guppyplex_docker String Internal component, do not modify Optional
read_QC_trim artic_guppyplex_memory Int Internal component, do not modify Optional
read_QC_trim call_kraken Boolean Internal component, do not modify FALSE Optional
read_QC_trim downsampling_coverage Float The desired coverage to sub-sample the reads to with RASUSA 150 Optional
read_QC_trim kraken2_recalculate_abundances_cpu Int Internal component, do not modify Optional
read_QC_trim kraken2_recalculate_abundances_disk_size Int Internal component, do not modify Optional
read_QC_trim kraken2_recalculate_abundances_docker String Internal component, do not modify Optional
read_QC_trim kraken2_recalculate_abundances_memory Int Internal component, do not modify Optional
read_QC_trim kraken_cpu Int Internal component, do not modify Optional
read_QC_trim kraken_db File Internal component, do not modify Optional
read_QC_trim kraken_disk_size Int Internal component, do not modify Optional
read_QC_trim kraken_docker_image String Internal component, do not modify Optional
read_QC_trim kraken_memory Int Internal component, do not modify Optional
read_QC_trim max_length Int Internal component, do not modify Optional
read_QC_trim min_length Int Internal component, do not modify Optional
read_QC_trim nanoq_cpu Int Number of CPUs to allocate to the task 2 Optional
read_QC_trim nanoq_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
read_QC_trim nanoq_docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/biocontainers/nanoq:0.9.0--hec16e2b_1 Optional
read_QC_trim nanoq_max_read_length Int The maximum read length to keep after trimming 100000 Optional
read_QC_trim nanoq_max_read_qual Int The maximum read quality to keep after trimming 40 Optional
read_QC_trim nanoq_memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
read_QC_trim nanoq_min_read_length Int The minimum read length to keep after trimming 500 Optional
read_QC_trim nanoq_min_read_qual Int The minimum read quality to keep after trimming 10 Optional
read_QC_trim ncbi_scrub_cpu Int Internal component, do not modify 4 Optional
read_QC_trim ncbi_scrub_disk_size Int Internal component, do not modify 100 Optional
read_QC_trim ncbi_scrub_docker String Internal component, do not modify us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1 Optional
read_QC_trim ncbi_scrub_memory Int Internal component, do not modify 8 Optional
read_QC_trim rasusa_bases String Explicitly set the number of bases required e.g., 4.3kb, 7Tb, 9000, 4.1MB. If this option is given, --coverage and --genome-size are ignored Optional
read_QC_trim rasusa_cpu Int Number of CPUs to allocate to the task 4 Optional
read_QC_trim rasusa_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
read_QC_trim rasusa_docker String Internal component, do not modify Optional
read_QC_trim rasusa_fraction_of_reads Float Subsample to a fraction of the reads - e.g., 0.5 samples half the reads Optional
read_QC_trim rasusa_memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
read_QC_trim rasusa_number_of_reads Int Subsample to a specific number of reads Optional
read_QC_trim rasusa_seed Int Random seed to use Optional
read_QC_trim run_prefix String Internal component, do not modify Optional
read_QC_trim target_organism String Internal component, do not modify Optional
theiaeuk_ont busco_docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.3.2_cv1 Optional
theiaeuk_ont busco_memory Int Amount of memory/RAM (in GB) to allocate to the task 24 Optional
theiaeuk_ont gambit_db_genomes File User-provided database of assembled query genomes; requires complementary signatures file. If not provided, uses default database, "/gambit-db" gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-metadata-1.0.0-20241213.gdb Optional
theiaeuk_ont gambit_db_signatures File User-provided signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used. gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-signatures-1.0.0-20241213.gs Optional
theiaeuk_ont genome_length Int User-specified expected genome length to be used in genome statistics calculations 50000000 Optional
theiaeuk_ont max_genome_length Int Maximum genome size able to pass read screening 178000000 Optional
theiaeuk_ont min_basepairs Int Minimum number of base pairs able to pass read screening 45000000 Optional
theiaeuk_ont min_coverage Int Minimum genome coverage able to pass read screening 5 Optional
theiaeuk_ont min_genome_length Int Minimum genome size able to pass read screening 9000000 Optional
theiaeuk_ont min_reads Int Minimum number of reads to pass read screening 5000 Optional
theiaeuk_ont skip_mash Boolean If true, skips estimation of genome size and coverage using mash in read screening steps. As a result, providing true also prevents screening using these parameters. TRUE Optional
theiaeuk_ont skip_screen Boolean Option to skip the read screening prior to analysis; if setting to true, please provide a value for the theiaeuk_pe genome_length optional input, OR set call_rasusa to false. Otherwise RASUSA will attempt to downsample to an expected genome size of 0 bp, and the workflow will fail. FALSE Optional
theiaeuk_ont workflow_series String Internal component, do not modify theiaeuk Optional
version_capture docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0 Optional
version_capture timezone String Set the time zone to get an accurate date of analysis (uses UTC by default) Optional

Workflow Tasks

All input reads are processed through "core tasks" in the TheiaEuk workflows. These undertake read trimming and assembly appropriate to the input data type, currently only Illumina paired-end data. TheiaEuk workflow subsequently launch default genome characterization modules for quality assessment, and additional taxa-specific characterization steps. When setting up the workflow, users may choose to use "optional tasks" or alternatives to tasks run in the workflow by default.

Core tasks

These tasks are performed regardless of organism. They include tasks that are performed regardless of and specific for the input data type. They perform read trimming and assembly appropriate to the input data type.

versioning: Version Capture

The versioning task captures the workflow version from the GitHub (code repository) version.

Version Capture Technical details

Links
Task task_versioning.wdl
screen: Total Raw Read Quantification and Genome Size Estimation

The screen task ensures the quantity of sequence data is sufficient to undertake genomic analysis. It uses fastq-scan and bash commands for quantification of reads and base pairs, and mash sketching to estimate the genome size and its coverage. At each step, the results are assessed relative to pass/fail criteria and thresholds that may be defined by optional user inputs. Samples are run through all threshold checks, regardless of failures, and the workflow will terminate after the screen task if any thresholds are not met:

  1. Total number of reads: A sample will fail the read screening task if its total number of reads is less than or equal to min_reads.
  2. The proportion of basepairs reads in the forward and reverse read files: A sample will fail the read screening if fewer than min_proportion basepairs are in either the reads1 or read2 files.
  3. Number of basepairs: A sample will fail the read screening if there are fewer than min_basepairs basepairs
  4. Estimated genome size: A sample will fail the read screening if the estimated genome size is smaller than min_genome_size or bigger than max_genome_size.
  5. Estimated genome coverage: A sample will fail the read screening if the estimated genome coverage is less than the min_coverage.

Read screening is undertaken on both the raw and cleaned reads. The task may be skipped by setting the skip_screen variable to true.

Default values vary between the PE, SE, and ONT workflows. The rationale for these default values can be found below. If two default values are shown, the first is for Illumina workflows and the second is for ONT.

| Variable | Rationale | | --- | --- | --- | | skip_screen | false | Set to true to skip the read screen from running. If you set this value to true, please provide a value for the theiaeuk_illumina_pe genome_length optional input, OR set the theiaeuk_illumina_pe call_rasusa optional input to false. Otherwise RASUSA will attempt to downsample to an expected genome size of 0 bp, and the workflow will fail. | | min_reads | 3000 | Calculated from the minimum number of base pairs required for 20x coverage of the Hansenula polymorpha genome, the smallest fungal genome as of 2015-04-02 (8.97 Mbp), divided by 300 (the longest Illumina read length) | | min_basepairs | 45000000 | Should be greater than 10x coverage of Hansenula polymorpha, the smallest fungal genome as of 2015-04-02 (8.97 Mbp) | | min_genome_length | 9000000 | Based on the Hansenula polymorpha genome - the smallest fungal genome as of 2015-04-02 (8.97 Mbp) | | max_genome_length | 178000000 | Based on the Cenococcum geophilum genome, the largest pathogenic fungal genome (177.57 Mbp), plus an additional 2 Mbp to cater for potential extra genomic material | | min_coverage | 10 | A bare-minimum average per base coverage across the genome required for genome characterization. Higher coverage would be required for high-quality phylogenetics.| | min_proportion | 40 | Neither read1 nor read2 files should have less than 40% of the total number of reads. For paired-end data only. |

Screen Technical Details

There is a single WDL task for read screening. The screen task is run twice, once for raw reads and once for clean reads.

Links
Task task_screen.wdl (PE sub-task)
task_screen.wdl (SE sub-task)
Rasusa: Read subsampling (optional, on by default)

To deactivate this task, set call_rasusa to false.

Rasusa is a tool to randomly subsample sequencing reads to a specified coverage without assuming that all reads are of equal length, making it especially suitable for long-read data while still being applicable to short-read data.

The Rasusa task performs subsampling on the input raw reads. By default, this task will subsample TheiaProk_ONT reads to a depth of 150X using an estimated genome length of 5 million basepairs (0.7 Mb higher than the average bacterial genome length), and TheiaEuk_ONT reads using an estimated genome length of 50 million basepairs. The estimated genome length can be changed by the user by providing a different value for the genome_length input parameter. The target subsampling depth can also be adjusted by modifying the subsample_coverage variable.

For TheiaEuk_Illumina_PE, the estimated genome length is determined by the read_screen task. Please note that the user can prevent the task from being launched by setting the call_rasusa variable to false.

Non-deterministic output(s)

This task may yield non-deterministic outputs since it performs random subsampling. To ensure reproducibility, set a a value for the rasusa_seed optional input variable.

Rasusa Technical Details

Links
Task task_rasusa.wdl
Software Source Code Rasusa on GitHub
Software Documentation Rasusa on GitHub
Original Publication(s) Rasusa: Randomly subsample sequencing reads to a specified coverage
read_QC_trim: Read Quality Trimming, Adapter Removal, Quantification, and Identification

read_QC_trim is a sub-workflow that removes low-quality reads, low-quality regions of reads, and sequencing adapters to improve data quality. It uses a number of tasks, described below. The differences between the PE and SE versions of the read_QC_trim sub-workflow lie in the default parameters, the use of two or one input read file(s), and the different output files.

Read quality trimming

read_processing with "trimmomatic" (default) or "fastp"

Either trimmomatic or fastp can be used for read-quality trimming. Trimmomatic is used by default.

To activate fastp, set the read_processing input parameter to "fastp".

These tasks are mutually exclusive.

Trimmomatic: Read Trimming

Trimmomatic trims low-quality regions of Illumina paired-end or single-end reads with a sliding window (with a default window size of 4, specified with trim_window_size), cutting once the average quality within the window falls below the trim_quality_trim_score (default of 20 for paired-end, 30 for single-end). The read is discarded if it is trimmed below trim_minlen (default of 75 for paired-end, 25 for single-end).

Trimmomatic Technical Details

Links
Task task_trimmomatic.wdl
Software Source Code Trimmomatic on GitHub
Software Documentation Trimmomatic Website
Original Publication(s) Trimmomatic: a flexible trimmer for Illumina sequence data
fastp: Read Trimming

fastp trims low-quality regions of Illumina paired-end or single-end reads with a sliding window (with a default window size of 4, specified with trim_window_size), cutting once the average quality within the window falls below the trim_quality_trim_score (default of 20 for paired-end, 30 for single-end). The read is discarded if it is trimmed below trim_minlen (default of 75 for paired-end, 25 for single-end).

fastp also has additional default parameters and features that are not a part of trimmomatic's default configuration.

fastp default read-trimming parameters
Parameter Explanation
-g enables polyG tail trimming
-5 20 enables read end-trimming
-3 20 enables read end-trimming
--detect_adapter_for_pe enables adapter-trimming only for paired-end reads

Additional arguments can be passed using the fastp_args optional parameter.

Trimmomatic and fastp Technical Details

Links
Task task_fastp.wdl
Software Source Code fastp on GitHub
Software Documentation fastp on GitHub
Original Publication(s) fastp: an ultra-fast all-in-one FASTQ preprocessor
BBDuk: Adapter Trimming and PhiX Removal

Adapters are manufactured oligonucleotide sequences attached to DNA fragments during the library preparation process. In Illumina sequencing, these adapter sequences are required for attaching reads to flow cells. You can read more about Illumina adapters here. For genome analysis, it's important to remove these sequences since they're not actually from your sample. If you don't remove them, the downstream analysis may be affected.

The bbduk task removes adapters from sequence reads. To do this:

  • Repair from the BBTools package reorders reads in paired fastq files to ensure the forward and reverse reads of a pair are in the same position in the two fastq files (it re-pairs).
  • BBDuk ("Bestus Bioinformaticus" Decontamination Using Kmers) is then used to trim the adapters and filter out all reads that have a 31-mer match to PhiX, which is commonly added to Illumina sequencing runs to monitor and/or improve overall run quality.

BBDuk Technical Details

Links
Task task_bbduk.wdl
Software Source Code BBMap on SourceForge
Software Documentation BBDuk Guide (archived)
Read Quantification

read_qc with "fastq-scan" (default) or "fastqc"

Either fastq-scan or fastqc can be used for read quantification. fastq-scan is used by default.

To activate fastqc, set the read_qc input parameter to "fastqc".

These tasks are mutually exclusive.

fastq-scan: Read Quantification

fastq-scan quantifies the forward and reverse reads in FASTQ files. For paired-end data, it also provide the total number of read pairs. This task is run once with raw reads as input and once with clean reads as input. If QC has been performed correctly, you should expect fewer clean reads than raw reads.

fastq-scan Technical Details

Links
Task task_fastq_scan.wdl
Software Source Code fastq-scan on GitHub
Software Documentation fastq-scan on GitHub
FastQC: Read Quantification

FastQC quantifies the forward and reverse reads in FASTQ files. For paired-end data, it also provide the total number of read pairs. This task is run once with raw reads as input and once with clean reads as input. If QC has been performed correctly, you should expect fewer clean reads than raw reads.

This tool also provides a graphical visualization of the read quality.

FastQC Technical Details

Links
Task task_fastqc.wdl
Software Source Code FastQC on Github
Software Documentation FastQC Website
Kraken2: Read Identification (optional)

To activate this task, set call_kraken to true and provide a value for kraken_db.

Kraken2 is a bioinformatics tool originally designed for metagenomic applications. It has additionally proven valuable for validating taxonomic assignments and checking contamination of single-species (e.g. bacterial isolate, eukaryotic isolate, viral isolate, etc.) whole genome sequence data.

Database-dependent

This workflow automatically uses a viral-specific Kraken2 database. This database was generated in-house from RefSeq's viral sequence collection and human genome GRCh38. It's available at gs://theiagen-public-resources-rp/reference_data/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz.

As an alternative to MIDAS (see above), the Kraken2 task can also be turned on through setting the call_kraken input variable as true for the identification of reads to detect contamination with non-target taxa.

A database must be provided if this optional module is activated, through the kraken_db optional input. A list of suggested databases can be found on Kraken2 standalone documentation.

Kraken2 Technical Details

Links
Task task_kraken2.wdl
Software Source Code Kraken2 on GitHub
Software Documentation Kraken2 Documentation
Original Publication(s) Improved metagenomic analysis with Kraken 2

read_QC_trim Technical Details

Links
Subworkflow wf_read_QC_trim_pe.wdl
wf_read_QC_trim_se.wdl
qc_check: Check QC Metrics Against User-Defined Thresholds (optional)

To activate this task, provide a qc_check_table as input.

The qc_check task compares generated QC metrics against user-defined thresholds for each metric. This task will run if the user provides a qc_check_table TSV file. If all QC metrics meet the threshold, the qc_check output variable will read QC_PASS. Otherwise, the output will read QC_NA if the task could not proceed or QC_ALERT followed by a string indicating what metric failed.

The qc_check task applies quality thresholds according to the sample taxa. The sample taxa is taken from the gambit_predicted_taxon value inferred by the GAMBIT module OR can be manually provided by the user using the expected_taxon workflow input.

Formatting the qc_check_table.tsv
  • The first column of the qc_check_table lists the organism that the task will assess and the header of this column must be "taxon".
  • Any genus or species can be included as a row of the qc_check_table. However, these taxa must uniquely match the sample taxa, meaning that the file can include multiple species from the same genus (Vibrio_cholerae and Vibrio_vulnificus), but not both a genus row and species within that genus (Vibrio and Vibrio cholerae). The taxa should be formatted with the first letter capitalized and underscores in lieu of spaces.
  • Each subsequent column indicates a QC metric and lists a threshold for each organism that will be checked. The column names must exactly match expected values, so we highly recommend copy and pasting the header from the template file below as a starting place.
Template qc_check_table.tsv files

Example Purposes Only

The QC threshold values shown in the file above are for example purposes only and should not be presumed to be sufficient for every dataset.

qc_check Technical Details

Links
Task task_qc_check_phb.wdl

These tasks assemble the reads into a de novo assembly and assess the quality of the assembly.

digger_denovo: De novo Assembly

De novo assembly is the process or product of attempting to reconstruct a genome from scratch (without prior knowledge of the genome) using sequence reads. Assembly of fungal genomes from short-reads will produce multiple contigs per chromosome rather than a single contiguous sequence for each chromosome.

In TheiaProk and TheiaEuk Illumina workflows, de novo assembly is performed for samples that have sufficient read quantity and quality using digger_denovo, a subworkflow based off of Shovill pipeline. The name "digger" is a nod to Shovill and SPAdes.

De novo Assembly

assembler with skesa (default), spades, or megahit

To activate a particular assembler, set the assembler input parameter to either skesa (default), spades, or megahit.

These tasks are mutually exclusive.

SKESA: De novo Assembly (default)

This task is activated by default.

SKESA (Strategic K-mer Extension for Scrupulous Assemblies) is a de novo assembler that is fairly conservative and introduces breaks in the genome at repeat regions. This leads to higher sequence quality but more fragmented assemblies, which, depending on the final analysis goal, can be either highly preferred or detrimental. Designed for Illumina reads and haploid genomes, SKESA is the default assembler in the digger_denovo subworkflow.

SKESA Technical Details

Links
Task task_skesa.wdl
Software Source Code SKESA on GitHub
Software Documentation SKESA on GitHub
Original Publication(s) SKESA: strategic k-mer externsion for scrupulous assemblies
SPAdes: De novo Assembly (alternative)

To activate this task, set assembler to spades.

SPAdes (St. Petersburg genome assembler) is a de novo assembly tool that uses de Bruijn graphs to assemble genomes from Illumina short reads.

In TheiaProk, SPAdes is run in --isolate mode, which is the recommended flag for high-coverage isolate and multi-cell Illumina data, which is typical of most bacterial sequencing projects. This method is optimized for improving assembly quality and decreasing runtime.

Non-deterministic output(s)

This task may yield non-deterministic outputs.

MetaviralSPAdes Technical Details

Links
Task task_spades.wdl
Software Source Code SPAdes on GitHub
Software Documentation SPAdes Manual
Original Publication(s) TheiaProk: SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
TheiaViral: MetaviralSPAdes: assembly of viruses from metagenomic data
MEGAHIT: De novo Assembly (alternative)

To activate this task, set assembler to megahit.

The MEGAHIT assembler is a fast and memory-efficient de novo assembler that can handle large datasets. While optimized for metagenomics, MEGAHIT also performs well on single-genome assemblies, making it a versatile choice for various assembly tasks.

MEGAHIT uses a multiple k-mer strategy that can be beneficial for assembling genomes with varying coverage levels, which is common in metagenomic samples. It constructs succinct de Bruijn graphs to efficiently represent the assembly process, allowing it to handle large and complex datasets with reduced memory usage.

Non-deterministic output(s)

This task may yield non-deterministic outputs.

MEGAHIT Technical Details

Links
Task task_megahit.wdl
Software Source Code MEGAHIT on GitHub
Software Documentation MEGAHIT on GitHub
Original Publication(s) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Assembly Polishing (optional)

To activate assembly polishing, set call_pilon to true.

bwa: Read Alignment to the Assembly

BWA (Burrow-Wheeler Aligner) is used to align the cleaned read files to generated assembly file in order to generate an alignment. The resulting BAM file is directly passed to the Pilon task to polish the assembly for errors.

BWA Technical Details

Links
Task task_bwa.wdl
Software Source Code BWA on GitHub
Software Documentation BWA Documentation
Original Publication(s) Fast and accurate short read alignment with Burrows-Wheeler transform
Pilon: Assembly Polishing

Pilon is a tool that uses read alignments to correct errors in an assembly.

The bwa-generated alignment of the read data to the assembly is used to identify inconsistences between the reads and the assembly in order to correct them. Pilon will attempt to fix individual base errors and small indels using the read data. This can improve the overall quality of the assembly, especially when the assembler has made mistakes due to sequencing errors or low coverage regions.

The default parameters were set to mimic the parameters used by Shovill: --fix bases --minq 60 --minqual 3 --mindepth 0.25. These can be modified by the user.

Pilon Technical Details

Links
Task task_pilon.wdl
Software Source Code Pilon on GitHub
Software Documentation Pilon Wiki
Original Publication(s) Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Contig Filtering (optional)
Filter Contigs: Contig Quality Control

To deactivate contig filtering, set run_filter_contigs to false.

This task filters the created contigs based on a default minimum length threshold of 200 bp and a minimum coverage of 2.0. It also eliminates homopolymer contigs (contigs of any length that consist of a single nucleotide).

Options are available to skip any of these filters by setting the respective parameters to false: filter_contigs_skip_length_filter, filter_contigs_skip_coverage_filter, and filter_contigs_skip_homopolymer_filter. The minimum length and coverage thresholds can be adjusted using the filter_contigs_min_length and filter_contigs_min_coverage parameters, respectively.

This ensures high-quality assemblies by retaining only contigs that meet specified criteria. Detailed metrics on contig counts and sequence lengths before and after filtering are provided in the output.

Filter Contigs Technical Details

Links
WDL Task task_filter_contigs.wdl

Digger-Denovo Technical Details

Links
Subworkflow wf_digger_denovo.wdl
quast: Assembly Quality Assessment

QUAST stands for QUality ASsessment Tool. It evaluates genome/metagenome assemblies by computing various metrics without a reference being necessary. It includes useful metrics such as number of contigs, length of the largest contig and N50.

QUAST Technical Details

Links
Task task_quast.wdl
Software Source Code QUAST on GitHub
Software Documentation QUAST Manual on SourceForge
Original Publication(s) QUAST: quality assessment tool for genome assemblies
CG-Pipeline: Assessment of Read Quality, and Estimation of Genome Coverage

Thecg_pipeline task generates metrics about read quality and estimates the coverage of the genome using the run_assembly_readMetrics.pl script from CG-Pipeline. The genome coverage estimates are calculated using both using raw and cleaned reads, using either a user-provided genome_size or the estimated genome length generated by QUAST.

CG-Pipeline Technical Details

The cg_pipeline task is run twice in this workflow, once with raw reads, and once with clean reads.

Links
Task task_cg_pipeline.wdl
Software Source Code CG-Pipeline on GitHub
Software Documentation CG-Pipeline on GitHub
Original Publication(s) A computational genomics pipeline for prokaryotic sequencing projects
read_QC_trim_ont: Read Quality Trimming, Quantification, and Identification

read_QC_trim_ont is a sub-workflow that filters low-quality reads and trims low-quality regions of reads. It uses several tasks, described below.

A note on estimated genome length

By default, the estimated genome length is set to 5 Mb, which is around 0.7 Mb higher than the average bacterial genome length, according to the information of thousands of NCBI bacterial assemblies collated here. This estimate can be overwritten by the user and is used by Rasusa.

Rasusa: Read Subsampling

Rasusa is a tool to randomly subsample sequencing reads to a specified coverage without assuming that all reads are of equal length, making it especially suitable for long-read data while still being applicable to short-read data.

The Rasusa task performs subsampling on the input raw reads. By default, this task will subsample TheiaProk_ONT reads to a depth of 150X using an estimated genome length of 5 million basepairs (0.7 Mb higher than the average bacterial genome length), and TheiaEuk_ONT reads using an estimated genome length of 50 million basepairs. The estimated genome length can be changed by the user by providing a different value for the genome_length input parameter. The target subsampling depth can also be adjusted by modifying the subsample_coverage variable.

Non-deterministic output(s)

This task may yield non-deterministic outputs since it performs random subsampling. To ensure reproducibility, set a a value for the rasusa_seed optional input variable.

Rasusa Technical Details

Links
Task task_rasusa.wdl
Software Source Code Rasusa on GitHub
Software Documentation Rasusa on GitHub
Original Publication(s) Rasusa: Randomly subsample sequencing reads to a specified coverage
Nanoq: Read Filtering

Reads are filtered by length and quality using nanoq. By default, sequences with less than 500 basepairs and quality scores lower than 10 are filtered out to improve assembly accuracy. These defaults are able to be modified by the user.

Nanoq Technical Details

Links
Task task_nanoq.wdl
Software Source Code Nanoq on GitHub
Software Documentation Nanoq Documentation
Original Publication(s) Nanoq: ultra-fast quality control for nanopore reads
Kraken2: Read Identification (optional)

To activate this task, set call_kraken to true and provide a value for kraken_db.

Kraken2 is a bioinformatics tool originally designed for metagenomic applications. It has additionally proven valuable for validating taxonomic assignments and checking contamination of single-species (e.g. bacterial isolate, eukaryotic isolate, viral isolate, etc.) whole genome sequence data.

Kraken2 is run on the raw read data.

Database-dependent

This workflow automatically uses a viral-specific Kraken2 database. This database was generated in-house from RefSeq's viral sequence collection and human genome GRCh38. It's available at gs://theiagen-public-resources-rp/reference_data/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz.

A database must be provided if this optional module is activated, through the kraken_db optional input. A list of suggested databases can be found on Kraken2 standalone documentation.

Kraken2 Technical Details

Links
Task task_kraken2.wdl
Software Source Code Kraken2 on GitHub
Software Documentation Kraken2 Documentation
Original Publication(s) Improved metagenomic analysis with Kraken 2
NanoPlot: Read Quantification

NanoPlot is used for the determination of mean quality scores, read lengths, and number of reads. This task is run once with raw reads as input and once with clean reads as input. If QC has been performed correctly, you should expect fewer clean reads than raw reads.

While this task currently is run outside of the read_QC_trim_ont workflow, it is being included here as it calculates statistics on the read data. This is done so that the actual assembly genome lengths can be used (if an estimated genome length is not provided by the user) to ensure the estimated coverage statistics are accurate.

NanoPlot Technical Details

Links
Task task_nanoplot.wdl
Software Source Code NanoPlot on GitHub
Software Documentation NanoPlot Documentation
Original Publication(s) NanoPack2: population-scale evaluation of long-read sequencing data

read_QC_trim_ont Technical Details

Links
Subworkflow wf_read_QC_trim_ont.wdl

These tasks assemble the reads into a de novo assembly and assess the quality of the assembly.

Flye: De novo Assembly

flye_denovo is a sub-workflow that performs de novo assembly using Flye for ONT data and supports additional polishing and visualization steps.

Ensure correct medaka model is selected if performing medaka polishing

In order to obtain the best results, the appropriate model must be set to match the sequencer's basecaller model; this string takes the format of {pore}_{device}_{caller variant}_{caller_version}. See also https://github.com/nanoporetech/medaka?tab=readme-ov-file#models. If flye is being run on legacy data the medaka model will likely be r941_min_hac_g507. Recently generated data will likely be suited by the default model of r1041_e82_400bps_sup_v5.0.0.

The detailed steps and tasks are as follows:

Porechop: Read Trimming (optional; off by default)

Read trimming is optional and can be enabled by setting the run_porchop input variable to true.

Porechop is a tool for finding and removing adapters from ONT data. Adapters on the ends of reads are trimmed, and when a read has an adapter in the middle, the read is split into two.

Porechop Technical Details

Links
WDL Task task_porechop.wdl
Software Source Code Porechop on GitHub
Software Documentation https://github.com/rrwick/Porechop#porechop
Flye: De novo Assembly

Flye is a de novo assembler for long read data using repeat graphs. Compared to de Bruijn graphs, which require exact k-mer matches, repeat graphs can use approximate matches which better tolerates the error rate of ONT data.

flye_read_type input parameter

This input parameter specifies the type of sequencing reads being used for assembly. This parameter significantly impacts the assembly process and should match the characteristics of your input data. Below are the available options:

Parameter Explanation
--nano-hq (default) Optimized for ONT high-quality reads, such as Guppy5+ SUP or Q20 (<5% error). Recommended for ONT reads processed with Guppy5 or newer
--nano-raw For ONT regular reads, pre-Guppy5 (<20% error)
--nano-corr ONT reads corrected with other methods (<3% error)
--pacbio-raw PacBio regular CLR reads (<20% error)
--pacbio-corr PacBio reads corrected with other methods (<3% error)
--pacbio-hifi PacBio HiFi reads (<1% error)

Refer to the Flye documentation for detailed guidance on selecting the appropriate flye_read_type based on your sequencing data and additional optional paramaters.

Non-deterministic output(s)

This task may yield non-deterministic outputs.

Flye Technical Details

Links
WDL Task task_flye.wdl
Software Source Code Flye on GitHub
Software Documentation Flye Documentation
Original Publication(s) Assembly of long, error-prone reads using repeat graphs
Bandage: Graph Visualization

Bandage creates de novo assembly graphs containing the assembled contigs and the connections between those contigs. These graphs are useful for visualizing the assembly structure, identifying potential misassemblies, and understanding the relationships between contigs.

Bandage Technical Details

Links
WDL Task task_bandage_plot.wdl
Software Source Code Bandage on GitHub
Software Documentation Bandage Documentation
Original Publication(s) Bandage: interactive visualization of de novo genome assemblies
Polypolish: Hybrid Assembly Polishing for ONT and Illumina data

If short reads are provided with the optional illumina_read1 and illumina_read2 inputs, Polypolish will use those short-reads to correct errors in the long-read assemblies. Uniquely, Polypolish uses the short-read alignments where each read is aligned to all possible locations, meaning that even repeat regions will have error correction.

Polypolish Technical Details

Links
Task task_polypolish.wdl
Software Source Code Polypolish on GitHub
Software Documentation Polypolish Documentation
Original Publication(s) Polypolish: short-read polishing of long-read bacterial genome assemblies
How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies
Medaka: Polishing of Flye assembly (default; optional)

Polishing is optional and can be skipped by setting the skip_polishing variable to true. If polishing is skipped, then neither Medaka or Racon will run.

Medaka is the default assembly polisher used in TheiaProk. Racon may be used alternatively, and if so, Medaka will not run. Medaka uses the raw reads to polish the assembly and generate a consensus sequence.

Importantly, Medaka requires knowing the model that was used to generate the read data. There are several ways to provide this information:

  • Automatic Model Selection: Automatically determines the most appropriate Medaka model based on the input data, ensuring optimal polishing results without manual intervention.
  • User-Specified Model Override: Allows users to specify a particular Medaka model if automatic selection does not yield the desired outcome or for specialized use cases.
  • Default Model: If both automatic model selection fails and no user-specified model is provided, Medaka defaults to the predefined fallback model r1041_e82_400bps_sup_v5.0.0.

Medaka Model Resolution Process

Medaka's automatic model selection uses the medaka tools resolve_model command to identify the appropriate model for polishing. This process relies on metadata embedded in the input file, which is typically generated by the basecaller. If the automatic selection fails to identify a suitable model, Medaka gracefully falls back to the default model to maintain workflow continuity. Users should verify the chosen model and consider specifying a model override if necessary.

Medaka Technical Details

Links
WDL Task task_medaka.wdl
Software Source Code Medaka on GitHub
Software Documentation Medaka Documentation
Racon: Polishing of Flye assembly (alternative; optional)

Polishing is optional and can be skipped by setting the skip_polishing variable to true. If polishing is skipped, then neither Medaka or Racon will run.

Racon is an alternative to using medaka for assembly polishing, and can be run by setting the polisher input to "racon". Racon is a consensus algorithm designed for refining raw de novo DNA assemblies generated from long, uncorrected sequencing reads.

Racon Technical Details

Links
WDL Task task_racon.wdl
Software Source Code Racon on GitHub
Software Documentation Racon Documentation
Original Publication(s) Fast and accurate de novo genome assembly from long uncorrected reads
Filter Contigs: Filter contigs below a threshold length and remove homopolymer contigs

This task filters the created contigs based on a user-defined minimum length threshold (default of 1000) and eliminates homopolymer contigs (contigs of any length that consist of a single nucleotide).

This ensures high-quality assemblies by retaining only contigs that meet specified criteria. Detailed metrics on contig counts and sequence lengths before and after filtering are provided in the output.

Filter Contigs Technical Details

Links
WDL Task task_filter_contigs.wdl
Dnaapler: Final Assembly Orientation

Dnaapler reorients contigs to start at specific reference points. Dnaapler supports the following modes, which can be indicated by filling the dnaapler_mode input variable with the desired mode. The default is all, which reorients contigs to start with dnaA, terL, repA, or COG1474.

  • all: Reorients contigs to start with dnaA, terL, repA, or COG1474 (Default)
  • chromosome: Reorients to begin with the dnaA chromosomal replication initiator gene, commonly used for bacterial chromosome assemblies.
  • plasmid: Reorients to start with the repA plasmid replication initiation gene, ideal for plasmid assemblie
  • phage: Reorients to start with the terL large terminase subunit gene, used for bacteriophage assemblies
  • archaea: Reorients to start with the COG1474 archaeal Orc1/cdc6 gene, relevant for archaeal assemblies
  • custom: Reorients based on a user-specified gene in amino acid FASTA format for experimental or unique workflows
  • mystery: Reorients to start with a random CDS for exploratory purposes
  • largest: Reorients to start with the largest CDS in the assembly, often useful for poorly annotated genomes
  • nearest: Reorients to start with the first CDS nearest to the sequence start, resolving CDS breakpoints
  • bulk: Processes multiple contigs to start with the desired start gene (dnaA, terL, repA, or custom)

Dnaapler Technical Details

Links
WDL Task task_dnaapler.wdl
Software Source Code Dnaapler on GitHub
Software Documentation Dnaapler Documentation
Original Publication(s) Dnaapler: a tool to reorient circular microbial genomes

Flye-Denovo Technical Details

Links
Subworkflow wf_flye_denovo.wdl

Organism-agnostic characterization

These tasks are performed regardless of the organism and provide quality control and taxonomic assignment.

GAMBIT: Taxon Assignment

GAMBIT determines the taxon of the genome assembly using a k-mer based approach to match the assembly sequence to the closest complete genome in a database, thereby predicting its identity. Sometimes, GAMBIT can confidently designate the organism to the species level. Other times, it is more conservative and assigns it to a higher taxonomic rank.

For additional details regarding the GAMBIT tool and a list of available GAMBIT databases for analysis, please consult the GAMBIT tool documentation.

GAMBIT Technical Details

Links
Task task_gambit.wdl
Software Source Code GAMBIT on GitHub
Software Documentation GAMBIT ReadTheDocs
Original Publication(s) GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification
BUSCO: Assembly Quality Assessment

BUSCO (Benchmarking Universal Single-Copy Orthologue) attempts to quantify the completeness and contamination of an assembly to generate quality assessment metrics. It uses taxa-specific databases containing genes that are all expected to occur in the given taxa, each in a single copy. BUSCO examines the presence or absence of these genes, whether they are fragmented, and whether they are duplicated (suggestive that additional copies came from contaminants).

BUSCO notation

Here is an example of BUSCO notation: C:99.1%[S:98.9%,D:0.2%],F:0.0%,M:0.9%,n:440. There are several abbreviations used in this output:

  • Complete (C) - genes are considered "complete" when their lengths are within two standard deviations of the BUSCO group mean length.
  • Single-copy (S) - genes that are complete and have only one copy.
  • Duplicated (D) - genes that are complete and have more than one copy.
  • Fragmented (F) - genes that are only partially recovered.
  • Missing (M) - genes that were not recovered at all.
  • Number of genes examined (n) - the number of genes examined.

A high equity assembly will use the appropriate database for the taxa, have high complete (C) and single-copy (S) percentages, and low duplicated (D), fragmented (F) and missing (M) percentages.

BUSCO Technical Details

Links
Task task_busco.wdl
Software Source Code BUSCO on GitLab
Software Documentation https://busco.ezlab.org/
Orginal publication BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Organism-specific characterization

The TheiaEuk workflow automatically activates taxa-specific tasks after identification of the relevant taxa using GAMBIT. Many of these taxa-specific tasks do not require any additional inputs from the user.

Candidozyma auris (also known as Candida auris)

Three tools can be deployed when Candidozyma auris/Candida auris is identified.

Cladetyping: clade determination

A custom GAMBIT database is created using six clade-specific Candidozyma auris reference genomes. Sequences undergo genomic signature comparison against this database, which then enables assignment to one of the six Candidozyma auris clades (Clade I to Clade VI) based on sequence similarity and phylogenetic relationships. This integrated approach ensures precise clade assignments, crucial for understanding the genetic diversity and epidemiology of Candidozyma auris.

See more information on the reference information for the six clades below:

Clade Genome Accession Assembly Name Strain BioSample Accession
Clade I GCA_002759435.3 Cand_auris_B8441_V3 B8441 SAMN05379624
Clade II GCA_003013715.2 ASM301371v2 B11220 SAMN05379608
Clade III GCA_002775015.1 Cand_auris_B11221_V1 B11221 SAMN05379609
Clade IV GCA_003014415.1 Cand_auris_B11243 B11243 SAMN05379619
Clade V GCA_016809505.1 ASM1680950v1 IFRC2087 SAMN11570381
Clade VI GCA_032714025.1 ASM3271402v1 F1580 SAMN36753179

Clade VI annotation

Clade VI does not have an available reference genome annotation at the time of adding the reference genome into Cladetyping. While Clade VI assignment is functional, downstream variant calling is not currently possible without an annotation. Users may provide a close relative annotation, such as Clade IV, though it is unknown if Clade VI variants can reliably be called with respect to such a reference.

Cauris_Cladetyper Technical Details

Links
Task task_cauris_cladetyper.wdl
Software Source Code GAMBIT on GitHub
Software Documentation GAMBIT Overview
Original Publication(s) GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification
TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization
amr_search: Antimicrobial Resistance Profiling (optional)

To activate this task, set run_amr_search to be true.

This task performs in silico antimicrobial resistance (AMR) profiling for supported species using AMRsearch, the primary tool used by Pathogenwatch to genotype and infer antimicrobial resistance (AMR) phenotypes from assembled microbial genomes.

AMRsearch screens against Pathogenwatch's library of curated genotypes and inferred phenotypes, developed in collaboration with community experts. Resistance phenotypes are determined based on both resistance genes and mutations, and the system accounts for interactions between multiple SNPs, genes, and suppressors. Predictions follow S/I/R classification (Sensitive, Intermediate, Resistant).

Currently, only a subset of species are supported by this task.

Supported Species

The following table shows the species name and the associated NCBI Code. If you are running AMR Search as part of TheiaProk and TheiaEuk, these codes will be automatically determined based on the GAMBIT predicted taxon, or the user-provided expected_taxon input.

Species NCBI Code
Neisseria gonorrhoeae 485
Staphylococcus aureus 1280
Salmonella Typhi 90370
Streptococcus pneumoniae 1313
Klebisiella 570
Escherichia 561
Mycobacterium tuberculosis 1773
Candida auris 498019
Vibrio cholerae 666
Campylobacter 194

Outputs:

  • JSON Output: Contains the complete AMR profile, including detailed resistance state, detected resistance genes/mutations, and supporting BLAST results.
  • CSV & PDF Tables: An incorporated Python script, parse_amr_json.py, extracts and formats results into a CSV file and PDF summary table for easier visualization.

amr_search Technical Details

Links
Task task_amr_search.wdl
Software Source Code AMRsearch on GitHub
Software Documentation AMRsearch on GitHub
Original Publication(s) PAARSNP: rapid genotypic resistance prediction for Neisseria gonorrhoeae
Snippy Variants: antifungal resistance detection

To detect mutations that may confer antifungal resistance, Snippy is used to find all variants relative to the clade-specific reference, then these variants are queried for product names associated with resistance. It's important to note that unlike amr_search, this task reports all variants found in the searched targets.

The genes in which there are known resistance-conferring mutations for this pathogen are:

  • FKS1
  • ERG11 (lanosterol 14-alpha demethylase)
  • FUR1 (uracil phosphoribosyltransferase)

We query Snippy results to see if any mutations were identified in those genes. By default, we automatically check for the following loci (which can be overwritten by the user). You will find the mutations next to the locus tag in the theiaeuk_snippy_variants_hits column corresponding gene name (see below):

TheiaEuk Search Term Corresponding Gene Name
B9J08_005340 ERG6
B9J08_000401 FLO8
B9J08_005343 Hypothetical protein (PSK74852)
B9J08_003102 MEC3
B9J08_003737 ERG3
lanosterol.14-alpha.demethylase ERG11
uracil.phosphoribosyltransferase FUR1
FKS1 FKS1

For example, one sample may have the following output for the theiaeuk_snippy_variants_hits column:

lanosterol.14-alpha.demethylase: lanosterol 14-alpha demethylase (missense_variant c.428A>G p.Lys143Arg; C:266 T:0),B9J08_000401: hypothetical protein (stop_gained c.424C>T p.Gln142*; A:70 G:0)

Based on this, we can tell that ERG11 has a missense variant at position 143 (Lysine to Arginine) and B9J08_000401 (which is FLO8) has a stop-gained variant at position 142 (Glutamine to Stop).

Known resistance-conferring mutations for Candidozyma auris

Mutations in these genes that are known to confer resistance are shown below

Organism Found in Gene name Gene locus AA mutation Drug Reference
Candidozyma auris Human ERG11 Y132F Fluconazole Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses
Candidozyma auris Human ERG11 K143R Fluconazole Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses
Candidozyma auris Human ERG11 F126T Fluconazole Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses
Candidozyma auris Human FKS1 S639P Micafungin Activity of CD101, a long-acting echinocandin, against clinical isolates of Candida auris
Candidozyma auris Human FKS1 S639P Caspofungin Activity of CD101, a long-acting echinocandin, against clinical isolates of Candida auris
Candidozyma auris Human FKS1 S639P Anidulafungin Activity of CD101, a long-acting echinocandin, against clinical isolates of Candida auris
Candidozyma auris Human FKS1 S639F Micafungin A multicentre study of antifungal susceptibility patterns among 350 Candida auris isolates (2009–17) in India: role of the ERG11 and FKS1 genes in azole and echinocandin resistance
Candidozyma auris Human FKS1 S639F Caspofungin A multicentre study of antifungal susceptibility patterns among 350 Candida auris isolates (2009–17) in India: role of the ERG11 and FKS1 genes in azole and echinocandin resistance
Candidozyma auris Human FKS1 S639F Anidulafungin A multicentre study of antifungal susceptibility patterns among 350 Candida auris isolates (2009–17) in India: role of the ERG11 and FKS1 genes in azole and echinocandin resistance
Candidozyma auris Human FUR1 CAMJ_004922 F211I 5-flucytosine Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris

Snippy Variants Technical Details

Links
Task task_snippy_variants.wdl
task_snippy_gene_query.wdl
Software Source Code Snippy on GitHub
Software Documentation Snippy on GitHub
Candida albicans

When this species is detected by the taxon ID tool, an antifungal resistance detection task is deployed.

Snippy Variants: antifungal resistance detection

To detect mutations that may confer antifungal resistance, Snippy is used to find all variants relative to the clade-specific reference, and these variants are queried for product names associated with resistance.

The genes in which there are known resistance-conferring mutations for this pathogen are:

  • ERG11
  • GCS1 (FKS1)
  • FUR1
  • RTA2

We query Snippy results to see if any mutations were identified in those genes. By default, we automatically check for the following loci (which can be overwritten by the user). You will find the mutations next to the locus tag in the theiaeuk_snippy_variants_hits column corresponding gene name (see below):

TheiaEuk Search Term Corresponding Gene Name
ERG11 ERG11
GCS1 FKS1
FUR1 FUR1
RTA2 RTA2

Snippy Variants Technical Details

Links
Task task_snippy_variants.wdl
task_snippy_gene_query.wdl
Software Source Code Snippy on GitHub
Software Documentation Snippy on GitHub
Aspergillus fumigatus

When this species is detected by the taxon ID tool an antifungal resistance detection task is deployed.

Snippy Variants: antifungal resistance detection

To detect mutations that may confer antifungal resistance, Snippy is used to find all variants relative to the clade-specific reference, and these variants are queried for product names associated with resistance.

The genes in which there are known resistance-conferring mutations for this pathogen are:

  • Cyp51A
  • HapE
  • COX10 (AFUA_4G08340)

We query Snippy results to see if any mutations were identified in those genes. By default, we automatically check for the following loci (which can be overwritten by the user). You will find the mutations next to the locus tag in the theiaeuk_snippy_variants_hits column corresponding gene name (see below):

TheiaEuk Search Term Corresponding Gene Name
Cyp51A Cyp51A
HapE HapE
AFUA_4G08340 COX10

Snippy Variants Technical Details

Links
Task task_snippy_variants.wdl
task_snippy_gene_query.wdl
Software Source Code Snippy on GitHub
Software Documentation Snippy on GitHub
Cryptococcus neoformans

When this species is detected by the taxon ID tool an antifungal resistance detection task is deployed.

Snippy Variants: antifungal resistance detection

To detect mutations that may confer antifungal resistance, Snippy is used to find all variants relative to the clade-specific reference, and these variants are queried for product names associated with resistance.

The genes in which there are known resistance-conferring mutations for this pathogen are:

  • ERG11 (CNA00300)

We query Snippy results to see if any mutations were identified in those genes. By default, we automatically check for the following loci (which can be overwritten by the user). You will find the mutations next to the locus tag in the theiaeuk_snippy_variants_hits column corresponding gene name (see below):

TheiaEuk Search Term Corresponding Gene Name
CNA00300 ERG11

Snippy Variants Technical Details

Links
Task task_snippy_variants.wdl
task_snippy_gene_query.wdl
Software Source Code Snippy on GitHub
Software Documentation Snippy on GitHub

Outputs

Variable Type Description
amr_search_csv File CSV formatted AMR profile
amr_search_docker String Docker image used to run AMR_Search
amr_search_results File JSON formatted AMR profile including BLAST results
amr_search_results_pdf File PDF formatted AMR profile
amr_search_version String Version of AMR_Search libraries used
assembler String Assembler used in digger_denovo subworkflow
assembler_version String Version of the assembler used in digger_denovo
assembly_fasta File De novo genome assembly in FASTA format
assembly_length Int Length of assembly (total contig length) as determined by QUAST
bbduk_docker String The Docker image for bbduk, which was used to remove the adapters from the sequences
busco_database String BUSCO database used
busco_docker String BUSCO docker image used
busco_report File A plain text summary of the results in BUSCO notation
busco_results String BUSCO results (see relevant toggle in this block)
busco_version String BUSCO software version used
cg_pipeline_docker String Docker file used for running CG-Pipeline on cleaned reads
cg_pipeline_report_clean File TSV file of read metrics from clean reads, including average read length, number of reads, and estimated genome coverage
cg_pipeline_report_raw File TSV file of read metrics from raw reads, including average read length, number of reads, and estimated genome coverage
cladetyper_annotated_reference String The annotated reference file for the identified clade, "None" if no clade was identified/no annotation is inputted
cladetyper_clade String The clade assigned to the input assembly
cladetyper_docker_image String The Docker container used for the task
cladetyper_gambit_version String The version of GAMBIT used for the analysis
combined_mean_q_clean Float Mean quality score for the combined clean reads
combined_mean_q_raw Float Mean quality score for the combined raw reads
combined_mean_readlength_clean Float Mean read length for the combined clean reads
combined_mean_readlength_raw Float Mean read length for the combined raw reads
contigs_gfa File Assembly graph output generated by SPAdes (Illumina: PE, SE) or Flye (ONT), used to visualize and evaluate genome assembly results.
est_coverage_clean Float Estimated coverage calculated from clean reads and genome length
est_coverage_raw Float Estimated coverage calculated from raw reads and genome length
fastp_html_report File The HTML report made with fastp
fastp_version String The version of fastp used
fastq_scan_clean1_json File The JSON file output from fastq-scan containing summary stats about clean forward read quality and length
fastq_scan_clean2_json File The JSON file output from fastq-scan containing summary stats about clean reverse read quality and length
fastq_scan_num_reads_clean1 Int The number of forward reads after cleaning as calculated by fastq_scan
fastq_scan_num_reads_clean2 Int The number of reverse reads after cleaning as calculated by fastq_scan
fastq_scan_num_reads_clean_pairs String The number of read pairs after cleaning as calculated by fastq_scan
fastq_scan_num_reads_raw1 Int The number of input forward reads as calculated by fastq_scan
fastq_scan_num_reads_raw2 Int The number of input reserve reads as calculated by fastq_scan
fastq_scan_num_reads_raw_pairs String The number of input read pairs as calculated by fastq_scan
fastq_scan_raw1_json File The JSON file output from fastq-scan containing summary stats about raw forward read quality and length
fastq_scan_raw2_json File The JSON file output from fastq-scan containing summary stats about raw reverse read quality and length
fastq_scan_version String The version of fastq_scan
fastqc_clean1_html File An HTML file that provides a graphical visualization of clean forward read quality from fastqc to open in an internet browser
fastqc_clean2_html File An HTML file that provides a graphical visualization of clean reverse read quality from fastqc to open in an internet browser
fastqc_docker String The Docker container used for fastqc
fastqc_num_reads_clean1 Int The number of forward reads after cleaning by fastqc
fastqc_num_reads_clean2 Int The number of reverse reads after cleaning by fastqc
fastqc_num_reads_clean_pairs String The number of read pairs after cleaning by fastqc
fastqc_num_reads_raw1 Int The number of input forward reads by fastqc before cleaning
fastqc_num_reads_raw2 Int The number of input reverse reads by fastqc before cleaning
fastqc_num_reads_raw_pairs String The number of input read pairs by fastqc before cleaning
fastqc_raw1_html File An HTML file that provides a graphical visualization of raw forward read quality from fastqc to open in an internet browser
fastqc_raw2_html File An HTML file that provides a graphical visualization of raw reverse read quality from fastqc to open in an internet browser
fastqc_version String Version of fastqc software used
filtered_contigs_metrics File File containing metrics of contigs filtered
gambit_closest_genomes File CSV file listing genomes in the GAMBIT database that are most similar to the query assembly
gambit_db_version String Version of the GAMBIT database used
gambit_docker String GAMBIT Docker used
gambit_predicted_taxon String Taxon predicted by GAMBIT
gambit_predicted_taxon_rank String Taxon rank of GAMBIT taxon prediction
gambit_report File GAMBIT report in a machine-readable format
gambit_version String Version of GAMBIT software used
n50_value Int N50 of assembly calculated by QUAST
number_contigs Int Total number of contigs in assembly
qc_check String A string that indicates whether or not the sample passes a set of pre-determined and user-provided QC thresholds
qc_standard File The file used in the QC Check task containing the QC thresholds.
quast_gc_percent Float The GC percent of your sample
quast_report File TSV report from QUAST
quast_version String The version of QUAST
r1_mean_q_raw Float Mean quality score of raw forward reads
r1_mean_readlength_raw Float Mean read length of raw forward reads
r2_mean_q_raw Float Mean quality score of raw reverse reads
r2_mean_readlength_raw Float Mean read length of raw reverse reads
rasusa_version String Version of RASUSA used for the analysis
read1_clean File Forward read file after quality trimming and adapter removal
read1_subsampled File Read1 FASTQ files downsampled to desired coverage
read2_clean File Reverse read file after quality trimming and adapter removal
read2_subsampled File Read2 FASTQ files downsampled to desired coverage
read_screen_clean String PASS or FAIL result from clean read screening; FAIL accompanied by the reason(s) for failure
read_screen_clean_tsv File Clean read screening report TSV depicting read counts, total read base pairs, and estimated genome length
read_screen_raw String PASS or FAIL result from raw read screening; FAIL accompanied by the reason(s) for failure
read_screen_raw_tsv File Raw read screening report TSV depicting read counts, total read base pairs, and estimated genome length
seq_platform String Description of the sequencing methodology used to generate the input read data
theiaeuk_illumina_pe_analysis_date String Date of TheiaEuk PE workflow execution
theiaeuk_illumina_pe_version String TheiaEuk PE workflow version used
theiaeuk_snippy_variants_bai String BAI file produced by the snippy module
theiaeuk_snippy_variants_bam String BAM file produced by the snippy module
theiaeuk_snippy_variants_coverage_tsv String TSV file containing coverage information for each base in the reference genome
theiaeuk_snippy_variants_gene_query_results String File containing all lines from variants file matching gene query terms
theiaeuk_snippy_variants_hits String String of all variant file entries matching gene query term
theiaeuk_snippy_variants_num_reads_aligned String Number of reads aligned by snippy
theiaeuk_snippy_variants_num_variants String Number of variants detected by snippy
theiaeuk_snippy_variants_outdir_tarball String Tar compressed file containing full snippy output directory
theiaeuk_snippy_variants_percent_ref_coverage String Percent of reference genome covered by snippy
theiaeuk_snippy_variants_query String The gene query term(s) used to search variant
theiaeuk_snippy_variants_query_check String Were the gene query terms present in the refence annotated genome file
theiaeuk_snippy_variants_reference_genome String The reference genome used in the alignment and variant calling
theiaeuk_snippy_variants_results String The variants file produced by snippy
theiaeuk_snippy_variants_summary String A file summarizing the variants detected by snippy
theiaeuk_snippy_variants_version String The version of the snippy_variants module being used
trimmomatic_docker String The docker image used for the trimmomatic module in this workflow
trimmomatic_version String The version of Trimmomatic used
Variable Type Description
amr_search_csv File CSV formatted AMR profile
amr_search_docker String Docker image used to run AMR_Search
amr_search_results File JSON formatted AMR profile including BLAST results
amr_search_results_pdf File PDF formatted AMR profile
amr_search_version String Version of AMR_Search libraries used
assembly_fasta File De novo genome assembly in FASTA format
assembly_length Int Length of assembly (total contig length) as determined by QUAST
bandage_plot File Image file (PNG) visualizing the Flye assembly graph generated by Bandage
bandage_version String Version of Bandage used
busco_database String BUSCO database used
busco_docker String BUSCO docker image used
busco_report File A plain text summary of the results in BUSCO notation
busco_results String BUSCO results (see relevant toggle in this block)
busco_version String BUSCO software version used
bwa_version String Version of BWA software used
cladetype_annotated_ref String The annotated reference file for the identified clade, "None" if no clade was identified/no annotation is inputted
cladetyper_clade String The clade assigned to the input assembly
cladetyper_docker_image String The Docker container used for the task
cladetyper_version String The version of Cladetyper used for the analysis
contigs_gfa File Assembly graph output generated by SPAdes (Illumina: PE, SE) or Flye (ONT), used to visualize and evaluate genome assembly results.
dnaapler_version String Version of dnaapler used
est_coverage_clean Float Estimated coverage calculated from clean reads and genome length
est_coverage_raw Float Estimated coverage calculated from raw reads and genome length
est_genome_length Int Estimated genome length
filtered_contigs_metrics File File containing metrics of contigs filtered
flye_assembly_info String Information file from Flye assembly
flye_version String Version of Flye software used
gambit_closest_genomes_file File CSV file listing genomes in the GAMBIT database that are most similar to the query assembly
gambit_db_version String Version of the GAMBIT database used
gambit_docker String GAMBIT Docker used
gambit_next_taxon String Next taxon predicted by GAMBIT
gambit_next_taxon_rank String Next taxon rank predicted by GAMBIT
gambit_predicted_taxon String Taxon predicted by GAMBIT
gambit_predicted_taxon_rank String Taxon rank of GAMBIT taxon prediction
gambit_report_file File GAMBIT report in a machine-readable format
gambit_version String Version of GAMBIT software used
medaka_model String Model used by Medaka
medaka_version String Version of Medaka used
merlin_tag String Merlin tag for the assembly
n50_value Int N50 of assembly calculated by QUAST
nanoplot_docker String Docker image for nanoplot
nanoplot_html_clean File An HTML report describing the clean reads
nanoplot_html_raw File An HTML report describing the raw reads
nanoplot_num_reads_clean1 Int Number of clean reads
nanoplot_num_reads_raw1 Int Number of raw reads
nanoplot_r1_est_coverage_clean Float Estimated coverage on the clean reads by nanoplot
nanoplot_r1_est_coverage_raw Float Estimated coverage on the raw reads by nanoplot
nanoplot_r1_mean_q_clean Float Mean quality score of clean forward reads
nanoplot_r1_mean_q_raw Float Mean quality score of raw forward reads
nanoplot_r1_mean_readlength_clean Float Mean read length of clean forward reads
nanoplot_r1_mean_readlength_raw Float Mean read length of raw forward reads
nanoplot_r1_median_q_clean Float Median quality score of clean forward reads
nanoplot_r1_median_q_raw Float Median quality score of raw forward reads
nanoplot_r1_median_readlength_clean Float Median read length of clean forward reads
nanoplot_r1_median_readlength_raw Float Median read length of raw forward reads
nanoplot_r1_n50_clean Float N50 of clean forward reads
nanoplot_r1_n50_raw Float N50 of raw forward reads
nanoplot_r1_stdev_readlength_clean Float Standard deviation read length of clean forward reads
nanoplot_r1_stdev_readlength_raw Float Standard deviation read length of raw forward reads
nanoplot_tsv_clean File A TSV report describing the clean reads
nanoplot_tsv_raw File A TSV report describing the raw reads
nanoplot_version String Version of nanoplot used for analysis
nanoq_version String Version of nanoq used in analysis
number_contigs Int Total number of contigs in assembly
polypolish_version String Version of Polypolish used
porechop_version String Version of Porechop used
quast_gc_percent Float The GC percent of your sample
quast_report File TSV report from QUAST
quast_version String The version of QUAST
racon_version String Version of Racon used
read1_clean File Forward read file after quality trimming and adapter removal
read_screen_clean String PASS or FAIL result from clean read screening; FAIL accompanied by the reason(s) for failure
read_screen_clean_tsv File Clean read screening report TSV depicting read counts, total read base pairs, and estimated genome length
read_screen_raw String PASS or FAIL result from raw read screening; FAIL accompanied by the reason(s) for failure
read_screen_raw_tsv File Raw read screening report TSV depicting read counts, total read base pairs, and estimated genome length
theiaeuk_ont_analysis_date String Date of TheiaEuk_ONT workflow execution
theiaeuk_ont_version String TheiaEuk_ONT workflow version used
theiaeuk_snippy_variants_bai String BAI file produced by the snippy module
theiaeuk_snippy_variants_bam String BAM file produced by the snippy module
theiaeuk_snippy_variants_coverage_tsv String TSV file containing coverage information for each base in the reference genome
theiaeuk_snippy_variants_gene_query_results String File containing all lines from variants file matching gene query terms
theiaeuk_snippy_variants_hits String String of all variant file entries matching gene query term
theiaeuk_snippy_variants_num_reads_aligned String Number of reads aligned by snippy
theiaeuk_snippy_variants_num_variants String Number of variants detected by snippy
theiaeuk_snippy_variants_outdir_tarball String Tar compressed file containing full snippy output directory
theiaeuk_snippy_variants_percent_ref_coverage String Percent of reference genome covered by snippy
theiaeuk_snippy_variants_query String The gene query term(s) used to search variant
theiaeuk_snippy_variants_query_check String Were the gene query terms present in the refence annotated genome file
theiaeuk_snippy_variants_results String The variants file produced by snippy
theiaeuk_snippy_variants_summary String A file summarizing the variants detected by snippy
theiaeuk_snippy_variants_version String The version of the snippy_variants module being used