TBProfiler_tNGS

Quick Facts

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level	Dockstore
Standalone	Bacteria, TB	v4.0.0	Yes	Sample-level	TBProfiler_tNGS_PHB

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	The name of the sample being analyzed		Required
clockwork_decon_reads	cpu	Int	Number of CPUs to allocate to the task	16	Optional
clockwork_decon_reads	disk_size	Int	Amount of storage (in GB) to allocate to the task	200	Optional
clockwork_decon_reads	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/cdcgov/varpipe_wgs_with_refs:2bc7234074bd53d9e92a1048b0485763cd9bbf6f4d12d5a1cc82bfec8ca7d75e	Optional
clockwork_decon_reads	memory	Int	Amount of memory (in GB) to allocate to the task	64	Optional
fastq_scan_clean	cpu	Int	Number of CPUs to allocate to the task	1	Optional
fastq_scan_clean	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional
fastq_scan_clean	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3	Optional
fastq_scan_clean	memory	Int	Amount of memory (in GB) to allocate to the task	4	Optional
fastq_scan_raw	cpu	Int	Number of CPUs to allocate to the task	1	Optional
fastq_scan_raw	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional
fastq_scan_raw	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3	Optional
fastq_scan_raw	memory	Int	Amount of memory (in GB) to allocate to the task	4	Optional
tbp_parser	add_cycloserine_lims	Boolean	Set to true add cycloserine results to the LIMS report	False	Optional
tbp_parser	config	File	The configuration file to use, in YAML format (overrides all other arguments except input_json and input_bam)		Optional
tbp_parser	coverage_regions_bed	File	A file that contains the regions to perform coverage analysis on		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:2.9.1	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_percent_coverage	Float	The minimum percentage of a region to exceed the minimum depth for a region to pass QC in tbp_parser	100	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	True	Optional
tbprofiler	additional_parameters	String	Additional parameters for TBProfiler		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	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:6.6.3	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_depth	Int	The minimum depth for a variant to be called.	10	Optional
tbprofiler	ont_data	Boolean	Specifies nanopore specific tbprofiler parameters	False	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		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.	gatk	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_tngs	run_clockwork	Boolean	Set to True to run Clockwork read decontamination	False	Optional
tbprofiler_tngs	run_trimmomatic	Boolean	Set to False to skip trimmomatic read trimming	True	Optional
tbprofiler_tngs	tbdb_branch	String	TBProfiler uses by default the TBDB database (a combination of the original library and the WHO v2 catalogue). You can opt to use a different mutation library by using this field to specify the name of the TBDB branch to use in TBProfiler; see the TBProfiler documentation for more information regarding available databases		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_base_crop	Int	Indicate the number of bases to remove from the start and end of the read (assuming average read length)		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
clockwork_decontaminated_read1	File	Decontaminated forward reads by Clockwork
clockwork_decontaminated_read2	File	Decontaminated reverse reads by Clockwork
clockwork_version	String	The version of Clockwork 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_clean_pairs	String	Number of read pairs after cleaning
fastq_scan_docker	String	The Docker image of fastq_scan
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_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_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_raw_pairs	String	Number of raw read pairs
fastq_scan_version	String	The version of fastq_scan
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 (sensitive, Pre-MDR, MDR, Pre-XDR, XDR)
tbprofiler_main_lineage	String	The Mycobacterium tuberculosis lineage assignment as made by TBProfiler
tbprofiler_median_depth	Float	The median depth of the H37Rv TB reference genome covered by the sample
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, in the format of <gene target> <variant detected> (<estimated fraction of reads that support the variant>)
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