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:2.2.2 |
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 |