Workflow: Tumor-Only Detect Variants workflow
Fetched 2023-01-14 20:32:37 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 | ||
| docm_vcf | File | ||
| vep_pick | |||
| reference | String | ||
| coding_only | Boolean (Optional) | ||
| sample_name | String | ||
| interval_list | File | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String | ||
| varscan_p_value | Float (Optional) | ||
| custom_gnomad_vcf | File (Optional) | ||
| varscan_min_reads | Integer (Optional) | ||
| vep_to_table_fields | String[] (Optional) | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float (Optional) | ||
| varscan_strand_filter | Integer (Optional) | ||
| variants_to_table_fields | String[] (Optional) | ||
| readcount_minimum_base_quality | Integer (Optional) | ||
| readcount_minimum_mapping_quality | Integer (Optional) | ||
| variants_to_table_genotype_fields | String[] (Optional) | ||
| maximum_population_allele_frequency | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| docm |
../subworkflows/docm_germline.cwl
(Workflow)
|
Detect DoCM variants | |
| index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| varscan |
../subworkflows/varscan_germline.cwl
(Workflow)
|
Varscan Workflow | |
| af_filter |
../tools/filter_vcf_gnomADe_allele_freq.cwl
(CommandLineTool)
|
gnomADe_AF filter | |
| decompose |
../tools/vt_decompose.cwl
(CommandLineTool)
|
run vt decompose | |
| cram_to_bam |
../subworkflows/cram_to_bam_and_index.cwl
(Workflow)
|
cram_to_bam workflow | |
| hard_filter |
../tools/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
| bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| bgzip_filtered |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| index_filtered |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| combine_variants |
../tools/germline_combine_variants.cwl
(CommandLineTool)
|
CombineVariants (GATK 3.6) | |
| annotate_variants |
../tools/vep.cwl
(CommandLineTool)
|
Ensembl Variant Effect Predictor | |
| variants_to_table |
../tools/variants_to_table.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
| coding_variant_filter |
../tools/filter_vcf_coding_variant.cwl
(CommandLineTool)
|
Coding Variant filter | |
| add_vep_fields_to_table |
../tools/add_vep_fields_to_table.cwl
(CommandLineTool)
|
add VEP annotation to report | |
| add_bam_readcount_to_vcf |
../subworkflows/vcf_readcount_annotator.cwl
(Workflow)
|
Add snv and indel bam-readcount files to a vcf |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| varscan_vcf | File | ||
| vep_summary | File | ||
| annotated_vcf | File | ||
| docm_gatk_vcf | File | ||
| tumor_snv_bam_readcount_tsv | File | ||
| tumor_indel_bam_readcount_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/4b5970dcf08bac2598e62ffd2673e67a25004c40/definitions/pipelines/tumor_only_detect_variants.cwl
