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download_and_compress_pipeline.cwl

Mattia Mancini authored
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download_and_compress_pipeline.cwl 1.81 KiB
class: Workflow
cwlVersion: v1.1
id: compress_pipeline_cwl
label: compress_pipeline.cwl
inputs:
- id: flag_autocorrelation
type: boolean?
- id: surls
type: 'string[]'
outputs:
- id: compressed
outputSource:
- compress/compressed
type: File[]
- id: logfile
outputSource:
- compress/logfile
type:
type: array
items:
type: array
items: File
- id: ingest
outputSource:
- compress/ingest
type: Any[]
- id: quality
type: Any
outputSource:
- format_quality_metrics/formatted_quality
- id: inspect
type: File
outputSource:
- combine/inspect_file
steps:
- id: fetch_data
in:
- id: surl_link
source: surls
out:
- id: uncompressed
run: steps/fetch_data.cwl
label: fetch_data
scatter:
- surl_link
- id: compress
in:
- id: msin
source: fetch_data/uncompressed
- id: flag_autocorrelation
source: flag_autocorrelation
scatter:
- msin
out:
- id: compressed
- id: inspect
- id: logfile
- id: ingest
run: ./compress_pipeline.cwl
- id: combine
in:
- id: inputs
source: compress/inspect
out:
- inspect_file
run: steps/combine_inspect_dataset.cwl
- id: extract_metrics
in:
- id: inspect
source: combine/inspect_file
out:
- id: plots
- id: quality
run: steps/extract_quality_metrics.cwl
- id: format_quality_metrics
in:
- id: plots
source: extract_metrics/plots
- id: quality
source: extract_metrics/quality
run: steps/format_metrics.cwl
out:
- formatted_quality
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement