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nucleo_qc.cwl
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nucleo_qc.cwl
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class: Workflow
cwlVersion: v1.0
id: nucleo_qc
doc: >-
This workflow generated all different quality control metrics and report for one or multiple samples
label: nucleo_qc
$namespaces:
s: 'https://schema.org/'
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: reference
type: File
'sbg:x': 0
'sbg:y': 747.90625
- id: target_intervals
type: File
'sbg:x': 0
'sbg:y': 106.84375
- id: bait_intervals
type: File
'sbg:x': 0
'sbg:y': 2136.875
- id: noise_sites_bed
type: File
'sbg:x': 0
'sbg:y': 961.59375
- id: biometrics_vcf_file
type: File
'sbg:x': 0
'sbg:y': 2030.03125
- id: biometrics_bed_file
type: File
'sbg:x': 0
'sbg:y': 2030.03125
- id: collapsed_bam
type: 'File[]'
'sbg:x': 0
'sbg:y': 1923.1875
- id: duplex_bam
type: 'File[]'
'sbg:x': 0
'sbg:y': 1816.34375
- id: group_reads_by_umi_bam
type: 'File[]'
'sbg:x': 0
'sbg:y': 1388.96875
- id: simplex_bam
type: 'File[]'
'sbg:x': 0
'sbg:y': 213.6875
- id: sample_sex
type: 'string[]?'
'sbg:x': 0
'sbg:y': 427.375
- id: sample_group
type: 'string[]'
'sbg:x': 0
'sbg:y': 641.0625
- id: uncollapsed_bam_base_recal
type: 'File[]'
'sbg:x': 0
'sbg:y': 0
- id: sample_name
type: 'string[]?'
'sbg:x': 0
'sbg:y': 534.21875
- id: samples-json
type: File
'sbg:x': 0
'sbg:y': 320.53125
- id: multiqc_config
type: File?
'sbg:x': 0
'sbg:y': 1068.4375
- id: hotspots_maf
type: File
'sbg:x': 0
'sbg:y': 1282.125
- id: mosdepth_bed
type: File?
'sbg:x': 0
'sbg:y': 1175.28125
- id: athena_transcript_file
type: File?
'sbg:x': 0
'sbg:y': 2350.5625
- id: athena_build
type: File?
'sbg:x': 0
'sbg:y': 3098.46875
- id: athena_flagstat
type: File?
'sbg:x': 0
'sbg:y': 2884.78125
- id: athena_thresholds
type: 'int[]?'
'sbg:x': 0
'sbg:y': 2457.40625
- id: athena_threshold
type: int?
'sbg:x': 0
'sbg:y': 2564.25
- id: athena_limit
type: int?
'sbg:x': 0
'sbg:y': 2777.9375
- id: athena_summary
type: boolean?
'sbg:x': 0
'sbg:y': 2671.09375
- id: athena_vcf
type: File?
'sbg:x': 0
'sbg:y': 2243.71875
- id: athena_cores
type: int?
'sbg:x': 0
'sbg:y': 2991.625
- id: output
type: 'string[]?'
'sbg:exposed': true
- id: omaf
type: boolean?
'sbg:x': 0
'sbg:y': 854.75
- id: generic_counting
type: boolean?
'sbg:x': 0
'sbg:y': 1495.8125
- id: fragment_count
type: int
'sbg:x': 0
'sbg:y': 1602.65625
- id: filter_duplicate
type: int
'sbg:x': 0
'sbg:y': 1709.5
outputs:
- id: multiqc_zip
outputSource:
- aggregate_visualize/multiqc_zip
type: File?
'sbg:x': 1599.148681640625
'sbg:y': 1442.390625
- id: multiqc_html
outputSource:
- aggregate_visualize/multiqc_html
type: File
'sbg:x': 1599.148681640625
'sbg:y': 1656.078125
- id: duplex_bam_biometrics_dir
outputSource:
- qc_generator/duplex_bam_biometrics_dir
type:
- Directory
- type: array
items: Directory
'sbg:x': 1076.5401611328125
'sbg:y': 1372.390625
- id: collapsed_bam_biometrics_dir
outputSource:
- qc_generator/collapsed_bam_biometrics_dir
type:
- Directory
- type: array
items: Directory
'sbg:x': 1076.5401611328125
'sbg:y': 1479.234375
- id: multiqc_output_dir
outputSource:
- aggregate_visualize/multiqc_output_dir
type: Directory
'sbg:x': 1599.148681640625
'sbg:y': 1549.234375
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: panel_bed
source: mosdepth_bed
- 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: duplex_biometrics_extract_pickle
- id: collapsed_biometrics_extract_pickle
- id: athena_coverage_report_dir
- 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': 288.796875
'sbg:y': 1360.234375
- id: aggregate_visualize
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: collapsed_extraction_files
source:
- qc_generator/collapsed_biometrics_extract_pickle
- id: uncollapsed_bam_stats_dir
source:
- qc_generator/uncollapsed_bam_stats_dir
- id: gatk_mean_quality_by_cycle_recal_dir
source:
- qc_generator/gatk_mean_quality_by_cycle_recal_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: collapsed_bam_duplex_metrics_dir
source:
- qc_generator/collapsed_bam_duplex_metrics_dir
- id: biometrics_extract_files_dir
source:
- qc_generator/biometrics_extract_files_dir
- id: samples-json
source: samples-json
- id: config
source: multiqc_config
- id: duplex_bam_sequence_qc_dir
source:
- qc_generator/duplex_bam_sequence_qc_dir
- id: athena_coverage_report_dir
source:
- qc_generator/athena_coverage_report_dir
out:
- id: multiqc_zip
- id: multiqc_html
- id: multiqc_output_dir
run: ./nucleo_aggregate_visualize.cwl
label: aggregate_visualize
'sbg:x': 1076.5401611328125
'sbg:y': 1656.078125
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 Charlambous
'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'