{"@id":"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl","retrievedFrom":{"repoUrl":"https://github.com/NCI-GDC/aliquot-maf-cwl.git","branch":"8390ae07f727491c10916024d31429a4b25c143b","path":"vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/NCI-GDC/aliquot-maf-cwl/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl","url":"https://github.com/NCI-GDC/aliquot-maf-cwl/blob/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl"},"retrievedOn":"2026-10-12T10:13:15.002+00:00","lastCommit":"8390ae07f727491c10916024d31429a4b25c143b","label":"vcf_to_aliquot_maf_wf.cwl","doc":"This copy is for use with the new merged panel of normals","inputs":{"job_uuid":{"type":"String"},"caller_id":{"type":"String"},"case_uuid":{"type":"String"},"sequencer":{"type":"String[]"},"maf_center":{"type":"String[]"},"min_n_depth":{"type":"Integer"},"context_size":{"type":"Integer"},"tumor_vcf_id":{"type":"String (Optional)"},"normal_vcf_id":{"type":"String (Optional)"},"upload_bucket":{"type":"String"},"tumor_bam_uuid":{"type":"String"},"cosmic_vcf_uuid":{"type":"String (Optional)"},"normal_bam_uuid":{"type":"String (Optional)"},"bioclient_config":{"type":"File"},"custom_enst_uuid":{"type":"String (Optional)"},"gdc_pon_vcf_uuid":{"type":"String (Optional)"},"gnomad_af_cutoff":{"type":"Float (Optional)"},"hotspot_tsv_uuid":{"type":"String (Optional)"},"annotated_vcf_uuid":{"type":"String"},"gdc_blacklist_uuid":{"type":"String (Optional)"},"maf_aliquot_schema":{"type":"String"},"tumor_aliquot_uuid":{"type":"String"},"tumor_submitter_id":{"type":"String"},"normal_aliquot_uuid":{"type":"String (Optional)"},"normal_submitter_id":{"type":"String (Optional)"},"effect_priority_uuid":{"type":"String"},"reference_fasta_uuid":{"type":"String"},"biotype_priority_uuid":{"type":"String"},"cosmic_vcf_index_uuid":{"type":"String (Optional)"},"experimental_strategy":{"type":"String"},"gdc_pon_vcf_index_uuid":{"type":"String (Optional)"},"target_intervals_record":{"type":"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/tools/schemas.cwl#indexed_file[]"},"annotated_vcf_index_uuid":{"type":"String"},"entrez_gene_id_json_uuid":{"type":"String"},"nonexonic_intervals_uuid":{"type":"String (Optional)"},"gnomad_noncancer_vcf_uuid":{"type":"String"},"reference_fasta_index_uuid":{"type":"String"},"nonexonic_intervals_index_uuid":{"type":"String (Optional)"},"gnomad_noncancer_vcf_index_uuid":{"type":"String"}},"outputs":{"aliquot_maf_uuid":{"type":"String"}},"steps":{"stage_data":{"run":"subworkflows/stage_data_workflow.vcf_to_aliquot_maf.cwl","runType":"WORKFLOW","sources":{"stage_data":{"sourceIDs":["reference_fasta_index_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/cosmic_vcf_uuid":{"sourceIDs":["cosmic_vcf_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/bioclient_config":{"sourceIDs":["bioclient_config"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/custom_enst_uuid":{"sourceIDs":["custom_enst_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/gdc_pon_vcf_uuid":{"sourceIDs":["gdc_pon_vcf_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/hotspot_tsv_uuid":{"sourceIDs":["hotspot_tsv_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/annotated_vcf_uuid":{"sourceIDs":["annotated_vcf_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/gdc_blacklist_uuid":{"sourceIDs":["gdc_blacklist_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/effect_priority_uuid":{"sourceIDs":["effect_priority_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/reference_fasta_uuid":{"sourceIDs":["reference_fasta_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/biotype_priority_uuid":{"sourceIDs":["biotype_priority_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/cosmic_vcf_index_uuid":{"sourceIDs":["cosmic_vcf_index_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/gdc_pon_vcf_index_uuid":{"sourceIDs":["gdc_pon_vcf_index_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/target_intervals_record":{"sourceIDs":["target_intervals_record"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/annotated_vcf_index_uuid":{"sourceIDs":["annotated_vcf_index_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/entrez_gene_id_json_uuid":{"sourceIDs":["entrez_gene_id_json_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/nonexonic_intervals_uuid":{"sourceIDs":["nonexonic_intervals_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/gnomad_noncancer_vcf_uuid":{"sourceIDs":["gnomad_noncancer_vcf_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/nonexonic_intervals_index_uuid":{"sourceIDs":["nonexonic_intervals_index_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#stage_data/gnomad_noncancer_vcf_index_uuid":{"sourceIDs":["gnomad_noncancer_vcf_index_uuid"]}}},"get_file_prefix":{"run":"../tools/make_file_prefix.cwl","runType":"EXPRESSIONTOOL","sources":{"get_file_prefix":{"sourceIDs":["caller_id"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#get_file_prefix/job_uuid":{"sourceIDs":["job_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#get_file_prefix/experimental_strategy":{"sourceIDs":["experimental_strategy"]}}},"make_aliquot_maf":{"run":"../tools/vcf_to_aliquot_maf.cwl","runType":"COMMANDLINETOOL","sources":{"make_aliquot_maf":{"sourceIDs":["tumor_bam_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/caller_id":{"sourceIDs":["caller_id"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/case_uuid":{"sourceIDs":["case_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/input_vcf":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/sequencer":{"sourceIDs":["sequencer"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/cosmic_vcf":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/maf_center":{"sourceIDs":["maf_center"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/maf_schema":{"sourceIDs":["maf_aliquot_schema"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/custom_enst":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/gdc_pon_vcf":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/hotspot_tsv":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/min_n_depth":{"sourceIDs":["min_n_depth"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/src_vcf_uuid":{"sourceIDs":["annotated_vcf_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/tumor_vcf_id":{"sourceIDs":["tumor_vcf_id"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/gdc_blacklist":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/normal_vcf_id":{"sourceIDs":["normal_vcf_id"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/normal_bam_uuid":{"sourceIDs":["normal_bam_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/output_filename":{"sourceIDs":["get_file_prefix"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/reference_fasta":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/gnomad_af_cutoff":{"sourceIDs":["gnomad_af_cutoff"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/target_intervals":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/tumor_aliquot_uuid":{"sourceIDs":["tumor_aliquot_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/tumor_submitter_id":{"sourceIDs":["tumor_submitter_id"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/entrez_gene_id_json":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/nonexonic_intervals":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/normal_aliquot_uuid":{"sourceIDs":["normal_aliquot_uuid"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/normal_submitter_id":{"sourceIDs":["normal_submitter_id"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/effect_priority_file":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/gnomad_noncancer_vcf":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/biotype_priority_file":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/reference_fasta_index":{"sourceIDs":["stage_data"]},"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl#make_aliquot_maf/reference_context_size":{"sourceIDs":["context_size"]}}}},"cwltoolVersion":"3.1.20230201224320","visualisationDot":"digraph workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"tumor_bam_uuid\" [fillcolor=\"#94DDF4\",label=\"tumor_bam_uuid\"];\n    \"job_uuid\" [fillcolor=\"#94DDF4\",label=\"job_uuid\"];\n    \"hotspot_tsv_uuid\" [fillcolor=\"#94DDF4\",label=\"hotspot_tsv_uuid\"];\n    \"normal_bam_uuid\" [fillcolor=\"#94DDF4\",label=\"normal_bam_uuid\"];\n    \"maf_aliquot_schema\" [fillcolor=\"#94DDF4\",label=\"maf_aliquot_schema\"];\n    \"normal_vcf_id\" [fillcolor=\"#94DDF4\",label=\"normal_vcf_id\"];\n    \"annotated_vcf_index_uuid\" [fillcolor=\"#94DDF4\",label=\"annotated_vcf_index_uuid\"];\n    \"caller_id\" [fillcolor=\"#94DDF4\",label=\"caller_id\"];\n    \"annotated_vcf_uuid\" [fillcolor=\"#94DDF4\",label=\"annotated_vcf_uuid\"];\n    \"sequencer\" [fillcolor=\"#94DDF4\",label=\"sequencer\"];\n    \"effect_priority_uuid\" [fillcolor=\"#94DDF4\",label=\"effect_priority_uuid\"];\n    \"reference_fasta_index_uuid\" [fillcolor=\"#94DDF4\",label=\"reference_fasta_index_uuid\"];\n    \"reference_fasta_uuid\" [fillcolor=\"#94DDF4\",label=\"reference_fasta_uuid\"];\n    \"custom_enst_uuid\" [fillcolor=\"#94DDF4\",label=\"custom_enst_uuid\"];\n    \"gdc_blacklist_uuid\" [fillcolor=\"#94DDF4\",label=\"gdc_blacklist_uuid\"];\n    \"context_size\" [fillcolor=\"#94DDF4\",label=\"context_size\"];\n    \"target_intervals_record\" [fillcolor=\"#94DDF4\",label=\"target_intervals_record\"];\n    \"cosmic_vcf_index_uuid\" [fillcolor=\"#94DDF4\",label=\"cosmic_vcf_index_uuid\"];\n    \"gnomad_noncancer_vcf_uuid\" [fillcolor=\"#94DDF4\",label=\"gnomad_noncancer_vcf_uuid\"];\n    \"normal_submitter_id\" [fillcolor=\"#94DDF4\",label=\"normal_submitter_id\"];\n    \"experimental_strategy\" [fillcolor=\"#94DDF4\",label=\"experimental_strategy\"];\n    \"min_n_depth\" [fillcolor=\"#94DDF4\",label=\"min_n_depth\"];\n    \"entrez_gene_id_json_uuid\" [fillcolor=\"#94DDF4\",label=\"entrez_gene_id_json_uuid\"];\n    \"gdc_pon_vcf_index_uuid\" [fillcolor=\"#94DDF4\",label=\"gdc_pon_vcf_index_uuid\"];\n    \"case_uuid\" [fillcolor=\"#94DDF4\",label=\"case_uuid\"];\n    \"tumor_vcf_id\" [fillcolor=\"#94DDF4\",label=\"tumor_vcf_id\"];\n    \"tumor_submitter_id\" [fillcolor=\"#94DDF4\",label=\"tumor_submitter_id\"];\n    \"bioclient_config\" [fillcolor=\"#94DDF4\",label=\"bioclient_config\"];\n    \"gnomad_noncancer_vcf_index_uuid\" [fillcolor=\"#94DDF4\",label=\"gnomad_noncancer_vcf_index_uuid\"];\n    \"gdc_pon_vcf_uuid\" [fillcolor=\"#94DDF4\",label=\"gdc_pon_vcf_uuid\"];\n    \"nonexonic_intervals_uuid\" [fillcolor=\"#94DDF4\",label=\"nonexonic_intervals_uuid\"];\n    \"upload_bucket\" [fillcolor=\"#94DDF4\",label=\"upload_bucket\"];\n    \"gnomad_af_cutoff\" [fillcolor=\"#94DDF4\",label=\"gnomad_af_cutoff\"];\n    \"cosmic_vcf_uuid\" [fillcolor=\"#94DDF4\",label=\"cosmic_vcf_uuid\"];\n    \"normal_aliquot_uuid\" [fillcolor=\"#94DDF4\",label=\"normal_aliquot_uuid\"];\n    \"tumor_aliquot_uuid\" [fillcolor=\"#94DDF4\",label=\"tumor_aliquot_uuid\"];\n    \"maf_center\" [fillcolor=\"#94DDF4\",label=\"maf_center\"];\n    \"biotype_priority_uuid\" [fillcolor=\"#94DDF4\",label=\"biotype_priority_uuid\"];\n    \"nonexonic_intervals_index_uuid\" [fillcolor=\"#94DDF4\",label=\"nonexonic_intervals_index_uuid\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"aliquot_maf_uuid\" [fillcolor=\"#94DDF4\",label=\"aliquot_maf_uuid\"];\n  }\n  \"make_aliquot_maf\" [label=\"make_aliquot_maf\"];\n  \"stage_data\" [label=\"stage_data\", fillcolor=\"#F3CEA1\"];\n  \"get_file_prefix\" [label=\"get_file_prefix\"];\n  \"default1\" -> \"emit_aliquot_maf\" [label=\"key\"];\n  \"default1\" [label=\"\\\"did\\\"\", fillcolor=\"#D5AEFC\"];\n  \"upload_aliquot_maf\" -> \"emit_aliquot_maf\" [label=\"input\"];\n  \"tumor_bam_uuid\" -> \"make_aliquot_maf\" [label=\"tumor_bam_uuid\"];\n  \"normal_bam_uuid\" -> \"make_aliquot_maf\" [label=\"normal_bam_uuid\"];\n  \"annotated_vcf_uuid\" -> \"make_aliquot_maf\" [label=\"src_vcf_uuid\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"gnomad_noncancer_vcf\"];\n  \"normal_vcf_id\" -> \"make_aliquot_maf\" [label=\"normal_vcf_id\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"reference_fasta_index\"];\n  \"min_n_depth\" -> \"make_aliquot_maf\" [label=\"min_n_depth\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"biotype_priority_file\"];\n  \"normal_aliquot_uuid\" -> \"make_aliquot_maf\" [label=\"normal_aliquot_uuid\"];\n  \"tumor_vcf_id\" -> \"make_aliquot_maf\" [label=\"tumor_vcf_id\"];\n  \"normal_submitter_id\" -> \"make_aliquot_maf\" [label=\"normal_submitter_id\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"target_intervals\"];\n  \"tumor_submitter_id\" -> \"make_aliquot_maf\" [label=\"tumor_submitter_id\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"hotspot_tsv\"];\n  \"maf_aliquot_schema\" -> \"make_aliquot_maf\" [label=\"maf_schema\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"entrez_gene_id_json\"];\n  \"maf_center\" -> \"make_aliquot_maf\" [label=\"maf_center\"];\n  \"sequencer\" -> \"make_aliquot_maf\" [label=\"sequencer\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"effect_priority_file\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"input_vcf\"];\n  \"case_uuid\" -> \"make_aliquot_maf\" [label=\"case_uuid\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"gdc_blacklist\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"nonexonic_intervals\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"custom_enst\"];\n  \"gnomad_af_cutoff\" -> \"make_aliquot_maf\" [label=\"gnomad_af_cutoff\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"cosmic_vcf\"];\n  \"caller_id\" -> \"make_aliquot_maf\" [label=\"caller_id\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"reference_fasta\"];\n  \"stage_data\" -> \"make_aliquot_maf\" [label=\"gdc_pon_vcf\"];\n  \"tumor_aliquot_uuid\" -> \"make_aliquot_maf\" [label=\"tumor_aliquot_uuid\"];\n  \"context_size\" -> \"make_aliquot_maf\" [label=\"reference_context_size\"];\n  \"get_file_prefix\" -> \"make_aliquot_maf\" [label=\"output_filename\"];\n  \"reference_fasta_index_uuid\" -> \"stage_data\" [label=\"reference_fasta_index_uuid\"];\n  \"reference_fasta_uuid\" -> \"stage_data\" [label=\"reference_fasta_uuid\"];\n  \"custom_enst_uuid\" -> \"stage_data\" [label=\"custom_enst_uuid\"];\n  \"gdc_blacklist_uuid\" -> \"stage_data\" [label=\"gdc_blacklist_uuid\"];\n  \"cosmic_vcf_index_uuid\" -> \"stage_data\" [label=\"cosmic_vcf_index_uuid\"];\n  \"hotspot_tsv_uuid\" -> \"stage_data\" [label=\"hotspot_tsv_uuid\"];\n  \"biotype_priority_uuid\" -> \"stage_data\" [label=\"biotype_priority_uuid\"];\n  \"effect_priority_uuid\" -> \"stage_data\" [label=\"effect_priority_uuid\"];\n  \"gdc_pon_vcf_index_uuid\" -> \"stage_data\" [label=\"gdc_pon_vcf_index_uuid\"];\n  \"target_intervals_record\" -> \"stage_data\" [label=\"target_intervals_record\"];\n  \"nonexonic_intervals_uuid\" -> \"stage_data\" [label=\"nonexonic_intervals_uuid\"];\n  \"gnomad_noncancer_vcf_index_uuid\" -> \"stage_data\" [label=\"gnomad_noncancer_vcf_index_uuid\"];\n  \"entrez_gene_id_json_uuid\" -> \"stage_data\" [label=\"entrez_gene_id_json_uuid\"];\n  \"annotated_vcf_index_uuid\" -> \"stage_data\" [label=\"annotated_vcf_index_uuid\"];\n  \"annotated_vcf_uuid\" -> \"stage_data\" [label=\"annotated_vcf_uuid\"];\n  \"cosmic_vcf_uuid\" -> \"stage_data\" [label=\"cosmic_vcf_uuid\"];\n  \"bioclient_config\" -> \"stage_data\" [label=\"bioclient_config\"];\n  \"nonexonic_intervals_index_uuid\" -> \"stage_data\" [label=\"nonexonic_intervals_index_uuid\"];\n  \"gdc_pon_vcf_uuid\" -> \"stage_data\" [label=\"gdc_pon_vcf_uuid\"];\n  \"gnomad_noncancer_vcf_uuid\" -> \"stage_data\" [label=\"gnomad_noncancer_vcf_uuid\"];\n  \"caller_id\" -> \"get_file_prefix\" [label=\"caller_id\"];\n  \"job_uuid\" -> \"get_file_prefix\" [label=\"job_uuid\"];\n  \"experimental_strategy\" -> \"get_file_prefix\" [label=\"experimental_strategy\"];\n  \"job_uuid\" -> \"upload_aliquot_maf\" [label=\"upload_key\"];\n  \"make_aliquot_maf\" -> \"upload_aliquot_maf\" [label=\"upload_key\"];\n  \"upload_bucket\" -> \"upload_aliquot_maf\" [label=\"upload_bucket\"];\n  \"make_aliquot_maf\" -> \"upload_aliquot_maf\" [label=\"input\"];\n  \"bioclient_config\" -> \"upload_aliquot_maf\" [label=\"config_file\"];\n  \"emit_aliquot_maf\" -> \"aliquot_maf_uuid\";\n}\n","licenseLink":"https://spdx.org/licenses/Apache-2.0","permalink":"https://w3id.org/cwl/view/git/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/NCI-GDC/aliquot-maf-cwl/blob/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl","visualisationPng":"/graph/png/github.com/NCI-GDC/aliquot-maf-cwl/blob/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl","visualisationSvg":"/graph/svg/github.com/NCI-GDC/aliquot-maf-cwl/blob/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl","roBundle":"/robundle/github.com/NCI-GDC/aliquot-maf-cwl/blob/8390ae07f727491c10916024d31429a4b25c143b/vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl","licenseName":"Apache License 2.0"}