Workflow: Subworkflow to allow calling different SV callers which require bam files as inputs
Fetched 2023-08-17 18:45:53 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 |
|---|---|---|---|
| bam | File | ||
| reference | String | ||
| cnvkit_method | String (Optional) | ||
| manta_non_wgs | Boolean (Optional) | ||
| merge_min_svs | Integer | ||
| vep_cache_dir | String | ||
| cnvkit_diagram | Boolean (Optional) | ||
| cnvkit_vcf_name | String (Optional) | ||
| merge_same_type | Boolean | ||
| merge_min_sv_size | Integer | ||
| merge_same_strand | Boolean | ||
| manta_call_regions | File (Optional) | ||
| merge_max_distance | Integer | ||
| cnvkit_scatter_plot | Boolean (Optional) | ||
| maximum_sv_pop_freq | Float (Optional) | ||
| 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[] (Optional) | ||
| cnvkit_reference_cnn | File | ||
| manta_output_contigs | Boolean (Optional) | ||
| merge_sv_pop_freq_db | File | ||
| vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
| cnvkit_male_reference | Boolean (Optional) | ||
| smoove_exclude_regions | File (Optional) | ||
| cnvkit_drop_low_coverage | Boolean (Optional) | ||
| sv_filter_interval_lists | https://w3id.org/cwl/view/git/a23f42ef49c10a588fd35a3afaad5de03e253533/definitions/types/labelled_file.yml#labelled_file[] | ||
| variants_to_table_fields | String[] (Optional) | ||
| merge_estimate_sv_distance | Boolean | ||
| variants_to_table_genotype_fields | String[] (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| run_manta |
../tools/manta_somatic.cwl
(CommandLineTool)
|
Set up and execute manta | |
| run_merge |
merge_svs.cwl
(Workflow)
|
merge and annotate svs with population allele freq and vep | |
| filter_vcf |
filter_sv_vcf.cwl
(Workflow)
|
SV filtering workflow | |
| run_cnvkit |
cnvkit_single_sample.cwl
(Workflow)
|
Subworkflow that runs cnvkit in single sample mode and returns a vcf file | |
| run_smoove |
../tools/smoove.cwl
(CommandLineTool)
|
Run Smoove v0.1.6 | |
| variants_to_table |
../tools/variants_to_table.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
| annotated_filter_bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| annotated_filter_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| add_vep_fields_to_table |
../tools/add_vep_fields_to_table.cwl
(CommandLineTool)
|
add VEP annotation to report |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cn_diagram | File (Optional) | ||
| cnvkit_vcf | File | ||
| filtered_vcfs | File[] | ||
| annotated_tsvs | File[] | ||
| cn_scatter_plot | File (Optional) | ||
| sv_pop_filtered_vcf | File | ||
| manta_all_candidates | File | ||
| merged_annotated_svs | File | ||
| tumor_target_coverage | File | ||
| manta_diploid_variants | File (Optional) | ||
| manta_small_candidates | File | ||
| manta_somatic_variants | File (Optional) | ||
| smoove_output_variants | File | ||
| tumor_bin_level_ratios | File | ||
| tumor_segmented_ratios | File | ||
| manta_tumor_only_variants | File (Optional) | ||
| tumor_antitarget_coverage | File |
Permalink:
https://w3id.org/cwl/view/git/a23f42ef49c10a588fd35a3afaad5de03e253533/definitions/subworkflows/single_sample_sv_callers.cwl
