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aggregate_visualize.cwl
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aggregate_visualize.cwl
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class: Workflow
cwlVersion: v1.0
id: aggregate_visualize
label: aggregate_visualize
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: duplex_extraction_files
type: 'File[]'
- id: collapsed_extraction_files
type: 'File[]'
- id: uncollapsed_bam_stats_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: simplex_bam_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: simplex_bam_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: gatk_mean_quality_by_cycle_recal_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: duplex_bam_stats_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: duplex_bam_stats_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: collapsed_bam_stats_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: collapsed_bam_stats_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: collapsed_bam_duplex_metrics_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: collapsed_bam_duplex_metrics_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: samples-json
type: File
- id: config
type: File?
- id: duplex_bam_sequence_qc_dir
type:
type: array
items:
- File
- Directory
- 'null'
- id: uncollapsed_bam_stats_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
outputs:
- id: multiqc_zip
outputSource:
- multiqc_1_10_1/multiqc_zip
type: File?
- id: multiqc_html
outputSource:
- multiqc_1_10_1/multiqc_html
type: File
- id: multiqc_output_dir
outputSource:
- multiqc_1_10_1/multiqc_output_dir
type: Directory
steps:
- id: qc_aggregator
in:
- id: duplex_extraction_files
source:
- duplex_extraction_files
- id: simplex_bam_pool_a_dir
source:
- simplex_bam_pool_a_dir
- id: simplex_bam_pool_b_dir
source:
- simplex_bam_pool_b_dir
- id: duplex_bam_sequence_qc_dir
source:
- duplex_bam_sequence_qc_dir
- id: duplex_bam_stats_pool_a_dir
source:
- duplex_bam_stats_pool_a_dir
- id: duplex_bam_stats_pool_b_dir
source:
- duplex_bam_stats_pool_b_dir
- id: collapsed_bam_stats_pool_a_dir
source:
- collapsed_bam_stats_pool_a_dir
- id: collapsed_bam_stats_pool_b_dir
source:
- collapsed_bam_stats_pool_b_dir
- id: collapsed_bam_duplex_metrics_pool_a_dir
source:
- collapsed_bam_duplex_metrics_pool_a_dir
- id: collapsed_bam_duplex_metrics_pool_b_dir
source:
- collapsed_bam_duplex_metrics_pool_b_dir
- id: gatk_mean_quality_by_cycle_recal_dir
source:
- gatk_mean_quality_by_cycle_recal_dir
- id: uncollapsed_bam_stats_pool_b_dir
source:
- uncollapsed_bam_stats_pool_b_dir
- id: uncollapsed_bam_stats_pool_a_dir
source:
- uncollapsed_bam_stats_pool_a_dir
- id: collapsed_extraction_files
source:
- collapsed_extraction_files
out:
- id: aggregate_qc_stats
run: qc_aggregator/qc_aggregator.cwl
label: qc_aggregator
- id: general_stats_parse
in:
- id: directory
source: qc_aggregator/aggregate_qc_stats
- id: samples-json
source: samples-json
- id: config
source: config
out:
- id: aggregate_parsed_stats
run: cwl-commandlinetools/access_utils/0.1.1/general_stats_parse.cwl
label: general_stats_parse
- id: multiqc_1_10_1
in:
- id: qc_files_dir
source: general_stats_parse/aggregate_parsed_stats
- id: config
source: config
out:
- id: multiqc_output_dir
- id: multiqc_html
- id: multiqc_zip
run: cwl-commandlinetools/multiqc/1.10.1.7/multiqc.cwl
requirements:
- class: SubworkflowFeatureRequirement