CWL Workflow: vcf_to_aliquot_maf_wf.cwl

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/0c2847431cc4dc5aae9379ff2bd221ba7d953e03/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

ID	Runs	Label	Doc
stage_data	subworkflows/stage_data_workflow.vcf_to_aliquot_maf.cwl (Workflow)
get_file_prefix	../tools/make_file_prefix.cwl (ExpressionTool)
make_aliquot_maf	../tools/vcf_to_aliquot_maf.cwl (CommandLineTool)

ID	Type	Label	Doc
aliquot_maf_uuid	String