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#!/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