- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
job_uuid | String | ||
caller_id | String | ||
case_uuid | String | ||
sequencer | String[] | ||
maf_center | String[] | ||
min_n_depth | Integer | ||
context_size | Integer | ||
tumor_vcf_id | String (Optional) | ||
normal_vcf_id | String (Optional) | ||
upload_bucket | String | ||
tumor_bam_uuid | String | ||
cosmic_vcf_uuid | String (Optional) | ||
normal_bam_uuid | String (Optional) | ||
bioclient_config | File | ||
custom_enst_uuid | String (Optional) | ||
gdc_pon_vcf_uuid | String (Optional) | ||
gnomad_af_cutoff | Float (Optional) | ||
hotspot_tsv_uuid | String (Optional) | ||
annotated_vcf_uuid | String | ||
gdc_blacklist_uuid | String (Optional) | ||
maf_aliquot_schema | String | ||
tumor_aliquot_uuid | String | ||
tumor_submitter_id | String | ||
normal_aliquot_uuid | String (Optional) | ||
normal_submitter_id | String (Optional) | ||
effect_priority_uuid | String | ||
reference_fasta_uuid | String | ||
biotype_priority_uuid | String | ||
cosmic_vcf_index_uuid | String (Optional) | ||
experimental_strategy | String | ||
gdc_pon_vcf_index_uuid | String (Optional) | ||
target_intervals_record | https://w3id.org/cwl/view/git/9aedc3fb22a3f5b9146bc5e9a393085050f90c95/tools/schemas.cwl#indexed_file[] | ||
annotated_vcf_index_uuid | String | ||
entrez_gene_id_json_uuid | String | ||
nonexonic_intervals_uuid | String (Optional) | ||
gnomad_noncancer_vcf_uuid | String | ||
reference_fasta_index_uuid | String | ||
nonexonic_intervals_index_uuid | String (Optional) | ||
gnomad_noncancer_vcf_index_uuid | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
stage_data | |||
get_file_prefix |
../tools/make_file_prefix.cwl
(ExpressionTool)
|
||
make_aliquot_maf |
../tools/vcf_to_aliquot_maf.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
aliquot_maf_uuid | String |
Permalink:
https://w3id.org/cwl/view/git/9aedc3fb22a3f5b9146bc5e9a393085050f90c95/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl