#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: InlineJavascriptRequirement inputs: - id: bam type: File - id: job_uuid type: string outputs: - id: output type: File outputSource: picard_markduplicates/OUTPUT - id: sqlite type: File outputSource: picard_markduplicates_to_sqlite/sqlite steps: - id: picard_markduplicates run: ../../tools/picard_markduplicates.cwl in: - id: INPUT source: bam out: - id: OUTPUT - id: METRICS - id: picard_markduplicates_to_sqlite run: ../../tools/picard_markduplicates_to_sqlite.cwl in: - id: bam source: bam valueFrom: $(self.basename) - id: input_state valueFrom: "markduplicates_readgroups" - id: metric_path source: picard_markduplicates/METRICS - id: job_uuid source: job_uuid out: - id: sqlite