| reference |
|
|
['string', 'File'] |
['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa'] |
| sequence |
sequence: sequencing data and readgroup information |
sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
../types/sequence_data.yml#sequence_data[] |
|
| trimming |
|
|
['../types/trimming_options.yml#trimming_options', 'null'] |
|
| omni_vcf |
|
|
File |
['.tbi'] |
| picard_metric_accumulation_level |
|
|
string |
|
| gvcf_gq_bands |
|
|
string[] |
|
| intervals |
|
|
{'type': 'array', 'items': {'type': 'array', 'items': 'string'}} |
|
| ploidy |
|
|
int? |
|
| qc_intervals |
|
|
File |
|
| variant_reporting_intervals |
|
|
File |
|
| vep_cache_dir |
|
|
['string', 'Directory'] |
|
| vep_ensembl_assembly |
|
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
string |
|
| vep_ensembl_version |
|
ensembl version - Must be present in the cache directory. Example: 95 |
string |
|
| vep_ensembl_species |
|
ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus |
string |
|
| vep_plugins |
|
array of plugins to use when running vep |
string[]? |
|
| synonyms_file |
|
|
File? |
|
| annotate_coding_only |
|
|
boolean? |
|
| bqsr_known_sites |
|
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
File[] |
['.tbi'] |
| bqsr_intervals |
|
|
string[]? |
|
| minimum_mapping_quality |
|
|
int? |
|
| minimum_base_quality |
|
|
int? |
|
| per_base_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| per_target_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| summary_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| vep_custom_annotations |
|
custom type, check types directory for input format |
../types/vep_custom_annotation.yml#vep_custom_annotation[] |
|
| cnvkit_diagram |
|
|
boolean? |
|
| cnvkit_drop_low_coverage |
|
|
boolean? |
|
| cnvkit_method |
|
|
['null', {'type': 'enum', 'symbols': ['hybrid', 'amplicon', 'wgs']}] |
|
| cnvkit_reference_cnn |
|
|
File? |
|
| cnvkit_scatter_plot |
|
|
boolean? |
|
| cnvkit_male_reference |
|
|
boolean? |
|
| cnvkit_vcf_name |
|
|
string? |
|
| manta_call_regions |
|
|
File? |
['.tbi'] |
| manta_non_wgs |
|
|
boolean? |
|
| manta_output_contigs |
|
|
boolean? |
|
| smoove_exclude_regions |
|
|
File? |
|
| merge_max_distance |
|
|
int |
|
| merge_min_svs |
|
|
int |
|
| merge_same_type |
|
|
boolean |
|
| merge_same_strand |
|
|
boolean |
|
| merge_estimate_sv_distance |
|
|
boolean |
|
| merge_min_sv_size |
|
|
int |
|
| sv_filter_alt_abundance_percentage |
|
|
double? |
|
| sv_filter_paired_count |
|
|
int? |
|
| sv_filter_split_count |
|
|
int? |
|
| cnv_filter_deletion_depth |
|
|
double? |
|
| cnv_filter_duplication_depth |
|
|
double? |
|
| variants_to_table_fields |
|
|
string[]? |
|
| variants_to_table_genotype_fields |
|
|
string[]? |
|
| vep_to_table_fields |
|
|
string[]? |
|
| cnv_filter_min_size |
|
|
int? |
|
| blocklist_bedpe |
|
|
File? |
|
| disclaimer_text |
|
|
string? |
|