Workflow: Subworkflow to allow calling different SV callers which require bam files as inputs
Fetched 2023-01-05 01:28:49 GMT
Verified with cwltool version 3.1.20221201130942
- 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 |
|---|---|---|---|
| cram | File | ||
| reference | String | ||
| cnvkit_method | String (Optional) | ||
| manta_non_wgs | Boolean (Optional) | ||
| cnvkit_diagram | Boolean (Optional) | ||
| cnvkit_vcf_name | String (Optional) | ||
| manta_call_regions | File (Optional) | ||
| cnvkit_scatter_plot | Boolean (Optional) | ||
| cnvkit_reference_cnn | File | ||
| manta_output_contigs | Boolean (Optional) | ||
| cnvkit_male_reference | Boolean (Optional) | ||
| smoove_exclude_regions | File (Optional) | ||
| cnvkit_drop_low_coverage | Boolean (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index_bam |
../tools/index_bam.cwl
(CommandLineTool)
|
samtools index | |
| run_manta |
../tools/manta_somatic.cwl
(CommandLineTool)
|
Set up and execute manta | |
| 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 | |
| cram_to_bam |
../tools/cram_to_bam.cwl
(CommandLineTool)
|
samtools view cram to bam |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cn_diagram | File (Optional) | ||
| cnvkit_vcf | File | ||
| cn_scatter_plot | File (Optional) | ||
| manta_all_candidates | 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/891c996dbd23d8154ec7609a56da3de841ae124c/definitions/subworkflows/single_sample_sv_callers.cwl
