Workflow: gathered exome alignment and somatic variant detection
Fetched 2023-01-10 09:41:21 GMT
Verified with cwltool version 3.1.20221201130942
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- Default Values
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
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 | ||
| interval_list | File | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String (Optional) | ||
| 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/233f026ffce240071edda526391be0c03186fce8/definitions/types/sequence_data.yml#sequence_data[] | ||
| hgvs_annotation | Boolean (Optional) | ||
| normal_sequence | https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/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 | ||
| summary_intervals | https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/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/233f026ffce240071edda526391be0c03186fce8/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/233f026ffce240071edda526391be0c03186fce8/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| 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[] |
Permalink:
https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/pipelines/somatic_exome_gathered.cwl
