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generate_aggregate.cwl
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generate_aggregate.cwl
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class: Workflow
cwlVersion: v1.0
id: generate_aggregate
label: generate_aggregate
$namespaces:
s: 'https://schema.org/'
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: reference
type: File
'sbg:x': 0
'sbg:y': 640.21875
- id: target_intervals
type: File
'sbg:x': 0
'sbg:y': 106.7109375
- id: bait_intervals
type: File
'sbg:x': 0
'sbg:y': 1920.609375
- id: noise_sites_bed
type: File
'sbg:x': 0
'sbg:y': 853.59375
- id: biometrics_vcf_file
type: File
'sbg:x': 0
'sbg:y': 1813.921875
- id: biometrics_bed_file
type: File
'sbg:x': 0
'sbg:y': 1813.921875
- id: collapsed_bam
type: 'File[]'
'sbg:x': 0
'sbg:y': 1707.234375
- id: duplex_bam
type: 'File[]'
'sbg:x': 0
'sbg:y': 1600.546875
- id: group_reads_by_umi_bam
type: 'File[]'
'sbg:x': 0
'sbg:y': 1173.6796875
- id: simplex_bam
type: 'File[]'
'sbg:x': 0
'sbg:y': 213.421875
- id: sample_sex
type: 'string[]?'
'sbg:x': 0
'sbg:y': 320.109375
- id: sample_group
type: 'string[]'
'sbg:x': 0
'sbg:y': 533.5078125
- id: uncollapsed_bam_base_recal
type: 'File[]'
'sbg:x': 0
'sbg:y': 0
- id: sample_name
type: 'string[]?'
'sbg:x': 0
'sbg:y': 426.796875
- id: hotspots_maf
type: File
'sbg:x': 0
'sbg:y': 1066.96875
- id: mosdepth_bed
type: File?
'sbg:x': 0
'sbg:y': 960.28125
- id: athena_transcript_file
type: File?
'sbg:x': 0
'sbg:y': 2133.984375
- id: athena_build
type: File?
'sbg:x': 0
'sbg:y': 2880.890625
- id: athena_flagstat
type: File?
'sbg:x': 0
'sbg:y': 2667.4921875
- id: athena_thresholds
type: 'int[]?'
'sbg:x': 0
'sbg:y': 2240.671875
- id: athena_threshold
type: int?
'sbg:x': 0
'sbg:y': 2347.359375
- id: athena_limit
type: int?
'sbg:x': 0
'sbg:y': 2560.78125
- id: athena_summary
type: boolean?
'sbg:x': 0
'sbg:y': 2454.0703125
- id: athena_vcf
type: File?
'sbg:x': 0
'sbg:y': 2027.296875
- id: athena_cores
type: int?
'sbg:x': 0
'sbg:y': 2774.203125
- id: output
type: 'string[]?'
'sbg:exposed': true
- id: omaf
type: boolean?
'sbg:x': 0
'sbg:y': 746.90625
- id: generic_counting
type: boolean?
'sbg:x': 0
'sbg:y': 1280.4140625
- id: fragment_count
type: int
'sbg:x': 0
'sbg:y': 1387.1484375
- id: filter_duplicate
type: int
'sbg:x': 0
'sbg:y': 1493.859375
outputs:
- id: duplex_bam_biometrics_dir
outputSource:
- qc_generator/duplex_bam_biometrics_dir
type:
- Directory
- type: array
items: Directory
'sbg:x': 803.9111938476562
'sbg:y': 1306.364990234375
- id: collapsed_bam_biometrics_dir
outputSource:
- qc_generator/collapsed_bam_biometrics_dir
type:
- Directory
- type: array
items: Directory
'sbg:x': 1076
'sbg:y': 1603.4080810546875
- id: aggregate_qc_stats
outputSource:
- qc_aggregator/aggregate_qc_stats
type: Directory
'sbg:x': 1585.9033203125
'sbg:y': 1440.421875
steps:
- id: qc_generator
in:
- id: reference
source: reference
- id: duplex_bam
source: duplex_bam
- id: collapsed_bam
source: collapsed_bam
- id: group_reads_by_umi_bam
source: group_reads_by_umi_bam
- id: uncollapsed_bam_base_recal
source: uncollapsed_bam_base_recal
- id: target_intervals
source: target_intervals
- id: bait_intervals
source: bait_intervals
- id: noise_sites_bed
source: noise_sites_bed
- id: sample_sex
source: sample_sex
- id: sample_name
source: sample_name
- id: sample_group
source: sample_group
- id: simplex_bam
source: simplex_bam
- id: vcf_file
source: biometrics_vcf_file
- id: biometrics_bed_file
source: biometrics_bed_file
- id: hotspots_maf
source: hotspots_maf
- id: mosdepth_bed
source: mosdepth_bed
- id: athena_transcript_file
source: athena_transcript_file
- id: athena_build
source: athena_build
- id: athena_flagstat
source: athena_flagstat
- id: athena_thresholds
source:
- athena_thresholds
- id: athena_threshold
source: athena_threshold
- id: athena_limit
source: athena_limit
- id: athena_summary
source: athena_summary
- id: athena_vcf
source: athena_vcf
- id: athena_cores
source: athena_cores
- id: output
source: output
- id: omaf
default: true
source: omaf
- id: generic_counting
source: generic_counting
- id: fragment_count
default: 1
source: fragment_count
- id: filter_duplicate
default: 0
source: filter_duplicate
out:
- id: uncollapsed_bam_stats_dir
- id: gatk_mean_quality_by_cycle_recal_dir
- id: collapsed_bam_biometrics_dir
- id: collapsed_bam_duplex_metrics_dir
- id: collapsed_bam_stats_dir
- id: simplex_bam_stats_dir
- id: duplex_bam_sequence_qc_dir
- id: duplex_bam_stats_dir
- id: duplex_bam_biometrics_dir
- id: athena_coverage_report_dir
- id: duplex_biometrics_extract_pickle
- id: collapsed_biometrics_extract_pickle
- id: biometrics_extract_files_dir
run: qc_generator/nucleo_qc_generator.cwl
label: qc_generator
scatter:
- duplex_bam
- collapsed_bam
- group_reads_by_umi_bam
- uncollapsed_bam_base_recal
- sample_sex
- sample_name
- sample_group
- simplex_bam
scatterMethod: dotproduct
'sbg:x': 288.8125
'sbg:y': 1251.421875
- id: qc_aggregator
in:
- id: duplex_extraction_files
source:
- qc_generator/duplex_biometrics_extract_pickle
- id: simplex_bam_stats_dir
source:
- qc_generator/simplex_bam_stats_dir
- id: duplex_bam_sequence_qc_dir
source:
- qc_generator/duplex_bam_sequence_qc_dir
- id: duplex_bam_stats_dir
source:
- qc_generator/duplex_bam_stats_dir
- id: collapsed_bam_stats_dir
source:
- qc_generator/collapsed_bam_stats_dir
- id: biometrics_extract_files_dir
source:
- qc_generator/biometrics_extract_files_dir
- id: collapsed_bam_duplex_metrics_dir
source:
- qc_generator/collapsed_bam_duplex_metrics_dir
- id: gatk_mean_quality_by_cycle_recal_dir
source:
- qc_generator/gatk_mean_quality_by_cycle_recal_dir
- id: uncollapsed_bam_stats_dir
source:
- qc_generator/uncollapsed_bam_stats_dir
- id: athena_coverage_report_dir
source:
- qc_generator/athena_coverage_report_dir
- id: collapsed_extraction_files
source:
- qc_generator/collapsed_biometrics_extract_pickle
out:
- id: aggregate_qc_stats
run: qc_aggregator/nucleo_qc_aggregator.cwl
label: qc_aggregator
'sbg:x': 1076.5557861328125
'sbg:y': 1270.734375
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: MultipleInputFeatureRequirement
$schemas:
- 'http://schema.org/version/latest/schemaorg-current-http.rdf'
's:author':
- class: 's:Person'
's:email': 'mailto:[email protected]'
's:identifier': ''
's:name': Carmelina Charalambous
's:citation': ''
's:codeRepository': 'https://github.com/msk-access/nucleo'
's:contributor':
- class: 's:Person'
's:email': 'mailto:[email protected]'
's:identifier': 'https://orcid.org/0000-0001-9042-6213'
's:name': Ronak Shah
's:dateCreated': '2020-11-23'
's:license': 'https://spdx.org/licenses/Apache-2.0'