#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: InlineJavascriptRequirement - class: StepInputExpressionRequirement - class: SubworkflowFeatureRequirement inputs: - id: bioclient_config type: File - id: bioclient_load_bucket type: string - id: input_bam_gdc_id type: string - id: input_bam_file_size type: long - id: start_token type: File - id: thread_count type: long - id: job_uuid type: string outputs: - id: indexd_sqlite_uuid type: string outputSource: emit_sqlite_uuid/output steps: - id: extract_bam run: ../../tools/bio_client_download.cwl in: - id: config-file source: bioclient_config - id: download_handle source: input_bam_gdc_id - id: file_size source: input_bam_file_size out: - id: output - id: transform run: transform.cwl in: - id: input_bam source: extract_bam/output - id: thread_count source: thread_count - id: job_uuid source: job_uuid out: - id: sqlite - id: load_sqlite run: ../../tools/bio_client_upload_pull_uuid.cwl in: - id: config-file source: bioclient_config - id: input source: transform/sqlite - id: upload-bucket source: bioclient_load_bucket - id: upload-key valueFrom: $(inputs.job_uuid)/$(inputs.input.basename) - id: job_uuid source: job_uuid valueFrom: $(null) out: - id: output - id: emit_sqlite_uuid run: ../../tools/emit_json_value.cwl in: - id: input source: load_sqlite/output - id: key valueFrom: did out: - id: output