Workflow: gathered exome alignment and somatic variant detection
Fetched 2023-01-10 11:48:29 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| mills | File | ||
| docm_vcf | File | ||
| omni_vcf | File | ||
| vep_pick | |||
| dbsnp_vcf | File | ||
| reference | File | ||
| cosmic_vcf | File (Optional) | ||
| output_dir | String | ||
| known_indels | File | ||
| somalier_vcf | File | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| known_variants | File (Optional) |
Previously discovered variants to be flagged in this pipelines's output vcf |
|
| tumor_sequence | https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/types/sequence_data.yml#sequence_data[] | ||
| hgvs_annotation | Boolean (Optional) | ||
| normal_sequence | https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/types/sequence_data.yml#sequence_data[] | ||
| tumor_cram_name | String (Optional) | ||
| varscan_p_value | Float (Optional) | ||
| normal_cram_name | String (Optional) | ||
| target_intervals | File | target_intervals: interval_list file of targets used in the sequencing experiment |
target_intervals is an interval_list corresponding to the targets for the capture reagent. Bed files with this information can be converted to interval_lists with Picard BedToIntervalList. In general for a WES exome reagent bait_intervals and target_intervals are the same. |
| summary_intervals | https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/types/labelled_file.yml#labelled_file[] | ||
| pindel_insert_size | Integer | ||
| vep_ensembl_species | String |
ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus |
|
| vep_ensembl_version | String |
ensembl version - Must be present in the cache directory. Example: 95 |
|
| vep_to_table_fields | String[] | ||
| annotate_coding_only | Boolean (Optional) | ||
| filter_docm_variants | Boolean (Optional) | ||
| mutect_scatter_count | Integer | ||
| panel_of_normals_vcf | File (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/types/labelled_file.yml#labelled_file[] | ||
| strelka_cpu_reserved | Integer (Optional) | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float (Optional) | ||
| vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
| varscan_strand_filter | Integer (Optional) | ||
| vep_custom_annotations | https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| target_interval_padding | Integer | target_interval_padding |
The effective coverage of capture products generally extends out beyond the actual regions targeted. This parameter allows variants to be called in these wingspan regions, extending this many base pairs from each side of the target regions. |
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| mutect_artifact_detection_mode | Boolean | ||
| picard_metric_accumulation_level | String | ||
| variants_to_table_genotype_fields | String[] | ||
| mutect_max_alt_alleles_in_normal_count | Integer (Optional) | ||
| mutect_max_alt_allele_in_normal_fraction | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gatherer |
../tools/gatherer.cwl
(CommandLineTool)
|
||
| somatic_exome |
somatic_exome.cwl
(Workflow)
|
somatic_exome: exome alignment and somatic variant detection |
somatic_exome is designed to perform processing of mutant/wildtype H.sapiens
exome sequencing data. It features BQSR corrected alignments, 4 caller variant
detection, and vep style annotations. Structural variants are detected via
manta and cnvkit. In addition QC metrics are run, including
somalier concordance metrics. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_outputs | String[] |
https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/pipelines/somatic_exome_gathered.cwl
