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etl.cwl
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etl.cwl
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#!/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