#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: InlineJavascriptRequirement inputs: - id: bam type: File - id: thread_count type: long outputs: - id: output type: File outputSource: samtools_index/output - id: sqlite type: File outputSource: format_sqlite/output steps: - id: samtools_index run: ../../tools/samtools_index.cwl in: - id: input source: bam - id: thread_count source: thread_count out: - id: output - id: empty_sqlite run: ../../tools/touch.cwl in: - id: input valueFrom: "empty.sqlite" out: - id: output - id: format_sqlite run: ../../tools/emit_file_format.cwl in: - id: input source: empty_sqlite/output - id: format valueFrom: "edam:format_2572" out: - id: output