Workflow: Subworkflow to allow calling different SV callers which require bam files as inputs
- 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 | ||
snps_vcf | File (Optional) | ||
reference | File | ||
genome_build | String | ||
cnvkit_method | |||
manta_non_wgs | Boolean (Optional) | ||
merge_min_svs | Integer | ||
cnvkit_diagram | Boolean (Optional) | ||
sv_split_count | Integer (Optional) | ||
blocklist_bedpe | File (Optional) | ||
cnvkit_vcf_name | String (Optional) | ||
merge_same_type | Boolean | ||
sv_paired_count | Integer (Optional) | ||
merge_min_sv_size | Integer | ||
merge_same_strand | Boolean | ||
cnv_deletion_depth | Double (Optional) | ||
manta_call_regions | File (Optional) | ||
merge_max_distance | Integer | ||
cnv_filter_min_size | Integer (Optional) | ||
cnvkit_scatter_plot | Boolean (Optional) | ||
cnvkit_reference_cnn | File (Optional) | ||
manta_output_contigs | Boolean (Optional) | ||
cnv_duplication_depth | Double (Optional) | ||
cnvkit_male_reference | Boolean (Optional) | ||
smoove_exclude_regions | File (Optional) | ||
cnvkit_drop_low_coverage | Boolean (Optional) | ||
merge_estimate_sv_distance | Boolean | ||
sv_alt_abundance_percentage | Double (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, annotate, and generate a TSV for SVs | |
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 v0.2.7 | |
run_cnvnator |
../tools/cnvnator.cwl
(CommandLineTool)
|
Run CNVnator to calculate copy number variations in WGS samples | |
run_manta_filter |
sv_paired_read_caller_filter.cwl
(Workflow)
|
Filter single sample sv vcf from paired read callers(Manta/Smoove) | |
run_cnvkit_filter |
sv_depth_caller_filter.cwl
(Workflow)
|
Filter single sample sv vcf from depth callers(cnvkit/cnvnator) | |
run_smoove_filter |
sv_paired_read_caller_filter.cwl
(Workflow)
|
Filter single sample sv vcf from paired read callers(Manta/Smoove) | |
run_cnvnator_filter |
sv_depth_caller_filter.cwl
(Workflow)
|
Filter single sample sv vcf from depth callers(cnvkit/cnvnator) | |
run_cnvkit_raw_bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
run_cnvkit_raw_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
run_cnvnator_raw_bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
run_cnvnator_raw_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
cn_diagram | File (Optional) | ||
cnvkit_vcf | File | ||
cnvnator_vcf | File | ||
cnvnator_root | File | ||
cn_scatter_plot | File (Optional) | ||
cnvnator_cn_file | File | ||
manta_filtered_vcf | File | ||
bcftools_merged_vcf | File | ||
cnvkit_filtered_vcf | File | ||
smoove_filtered_vcf | File | ||
survivor_merged_vcf | File | ||
manta_all_candidates | File | ||
cnvnator_filtered_vcf | 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 | ||
bcftools_merged_annotated_tsv | File | ||
survivor_merged_annotated_tsv | File | ||
bcftools_merged_filtered_annotated_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/a08de598edc04f340fdbff76c9a92336a7702022/definitions/subworkflows/single_sample_sv_callers.cwl