TBProfiler_tNGS

Quick Facts

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level
Standalone	Bacteria	PHB v2.0.0	Yes	Sample-level

TBProfiler_tNGS_PHB

This workflow is still in experimental research stages. Documentation is minimal as changes may occur in the code; it will be fleshed out when a stable state has been achieved.

Inputs

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
tbprofiler_tngs	read1	File	Illumina forward read file in FASTQ file format (compression optional)		Required
tbprofiler_tngs	read2	File	Illumina reverse read file in FASTQ file format (compression optional)		Required
tbprofiler_tngs	samplename	String	Name of sample to be analyzed		Required
tbp_parser	coverage_regions_bed	File	A file that contains the regions to perform coverage analysis on		Optional
tbp_parser	coverage_threshold	Int	The minimum percentage of a region to exceed the minimum depth for a region to pass QC in tbp_parser	100	Optional
tbp_parser	cpu	Int	Number of CPUs to allocate to the task	1	Optional
tbp_parser	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
tbp_parser	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.6.0	Optional
tbp_parser	etha237_frequency	Float	Minimum frequency for a mutation in ethA at protein position 237 to pass QC in tbp-parser	0.1	Optional
tbp_parser	expert_rule_regions_bed	File	A file that contains the regions where R mutations and expert rules are applied		Optional
tbp_parser	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional
tbp_parser	min_depth	Int	Minimum depth for a variant to pass QC in tbp_parser	10	Optional
tbp_parser	min_frequency	Float	Minimum allele frequency for a variant to pass QC in tbp-parser	0.1	Optional
tbp_parser	min_read_support	Int	Minimum read support for a variant to pass QC in tbp-parser	10	Optional
tbp_parser	operator	String	Fills the "operator" field in the tbp_parser output files		Optional
tbp_parser	rpob449_frequency	Float	Minimum frequency for a mutation at protein position 449 to pass QC in tbp-parser	0.1	Optional
tbp_parser	rrl_frequency	Float	Minimum frequency for a mutation in rrl to pass QC in tbp-parser	0.1	Optional
tbp_parser	rrl_read_support	Int	Minimum read support for a mutation in rrl to pass QC in tbp-parser	10	Optional
tbp_parser	rrs_frequency	Float	Minimum frequency for a mutation in rrs to pass QC in tbp-parser	0.1	Optional
tbp_parser	rrs_read_support	Int	Minimum read support for a mutation in rrs to pass QC in tbp-parser	10	Optional
tbp_parser	sequencing_method	String	Fills out the "seq_method" field in the tbp_parser output files		Optional
tbp_parser	tbp_parser_debug	Boolean	Activate the debug mode on tbp_parser; increases logging outputs	FALSE	Optional
tbprofiler	cov_frac_threshold	Int	A cutoff used to calculate the fraction of the region covered by ≤ this value	1	Optional
tbprofiler	cpu	Int	Number of CPUs to allocate to the task	8	Optional
tbprofiler	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
tbprofiler	mapper	String	The mapping tool used in TBProfiler to align the reads to the reference genome; see TBProfiler's original documentation for available options.	bwa	Optional
tbprofiler	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional
tbprofiler	min_af	Float	The minimum allele frequency to call a variant	0.1	Optional
tbprofiler	min_af_pred	Float	The minimum allele frequency to use a variant for resistance prediction	0.1	Optional
tbprofiler	min_depth	Int	The minimum depth for a variant to be called.	10	Optional
tbprofiler	ont_data	Boolean	Internal component; do not modify		Do not modify, Optional
tbprofiler	tbprofiler_custom_db	File	TBProfiler uses by default the TBDB database; if you have a custom database you wish to use, you must provide a custom database in this field and set tbprofiler_run_custom_db to true		Optional
tbprofiler	tbprofiler_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:4.4.2	Optional
tbprofiler	tbprofiler_run_custom_db	Boolean		FALSE	Optional
tbprofiler	variant_caller	String	Select a different variant caller for TBProfiler to use by writing it in this block; see TBProfiler's original documentation for available options.	freebayes	Optional
tbprofiler	variant_calling_params	String	Enter additional variant calling parameters in this free text input to customize how the variant caller works in TBProfiler		Optional
tbprofiler	bases_to_crop	Int	Indicate the number of bases to remove from the start and end of the read	30	Optional
trimmomatic_pe	cpu	Int	Number of CPUs to allocate to the task	4	Optional
trimmomatic_pe	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
trimmomatic_pe	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/trimmomatic:0.39	Optional
trimmomatic_pe	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional
trimmomatic_pe	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
trimmomatic_pe	trimmomatic_min_length	Int	Specifies minimum length of each read after trimming to be kept	75	Optional
trimmomatic_pe	trimmomatic_quality_trim_score	Int	The trimming quality score	30	Optional
trimmomatic_pe	trimmomatic_window_size	Int	The window size for trimming	4	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 Outputs

Variable	Type	Description
tbp_parser_average_genome_depth	Float	The mean depth of coverage across all target regions included in the analysis
tbp_parser_coverage_report	File	A file containing the breadth of coverage across each target loci
tbp_parser_docker	String	The docker image and version tag for the tbp_parser tool
tbp_parser_genome_percent_coverage	Float	The percent breadth of coverage across the entire genome
tbp_parser_laboratorian_report_csv	File	An output file containing information regarding each mutation and its associated drug resistance profile in a CSV file. This file also contains two interpretation fields -- "Looker" and "MDL" which are generated using the CDC's expert rules for interpreting the severity of potential drug resistance mutations.
tbp_parser_lims_report_csv	File	An output file formatted specifically for STAR LIMS. This CSV report summarizes the highest severity mutations for each antimicrobial and lists the relevant mutations for each gene.
tbp_parser_looker_report_csv	File	An output file that contains condensed information suitable for generating a dashboard in Google's Looker studio.
tbp_parser_version	String	The version number of tbp_parser
tbprofiler_dr_type	String	The drug resistance category as determined by TBProfiler
tbprofiler_main_lineage	String	The Mycobacterium tuberculosis lineage assignment as made by TBProfiler
tbprofiler_median_coverage	Int	The median depth of coverage across the target loci
tbprofiler_num_dr_variants	String	The total number of drug resistance conferring variants detected by TBProfiler
tbprofiler_num_other_variants	String	The total number of non-drug resistance conferring variants detected by TBProfiler
tbprofiler_output_alignment_bai	File	The index file associated with the binary alignment map of the input reads against the H37Rv genome
tbprofiler_output_alignment_bam	File	The binary alignment map of the input reads against the H37Rv genome
tbprofiler_pct_reads_mapped	Float	The percentage of reads that successfully mapped to the H37Rv genome
tbprofiler_report_csv	File	The raw output file from TBProfiler
tbprofiler_report_json	File	The json output file from TBProfiler
tbprofiler_report_tsv	File	The TSV output file from TBProfiler
tbprofiler_resistance_genes	String	The genes in which a mutation was detected that may be resistance conferring
tbprofiler_sub_lineage	String	The Mycobacterium tuberculosis sub-lineage assignment as made by TBProfiler
tbprofiler_tngs_wf_analysis_date	String	The date on which the workflow was run
tbprofiler_tngs_wf_version	String	The version of the tbprofiler_tngs workflow used for this analysis
tbprofiler_version	String	The version of TBProfiler used for this analysis
trimmomatic_docker	String	The docker image used for the trimmomatic module in this workflow
trimmomatic_read1_trimmed	File	The read1 file post trimming
trimmomatic_read2_trimmed	File	The read2 file post trimming
trimmomatic_stats	File	The read trimming statistics
trimmomatic_version	String	The version of trimmomatic used in this analysis