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ionox0/access_qc_aggregator.cwl

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access_qc_aggregator.cwl
Raw
access_qc_aggregator.cwl
class: Workflow
cwlVersion: v1.0
id: access_qc_aggregator
label: access_qc_aggregator
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: duplex_extraction_files
type:
type: array
items: File
inputBinding:
position: 0
prefix: '--input'
label: duplex_extraction_files
doc: >-
Can be one of three types: (1) path to a CSV file containing sample
information (one per line). For example:
sample_name,sample_bam,sample_type,sample_sex,sample_group. (2) Path to a
'*.pk' file that was produced by the 'extract' tool. (3) Name of the
sample to analyze; this assumes there is a file named '{sample_name}.pk'
in your database directory. Can be specified more than once.
'sbg:x': 0
'sbg:y': 533.671875
- id: duplex_biometrics_discordance_threshold
type: float?
doc: >-
Discordance values less than this are regarded as matching samples.
(default: 0.05)
'sbg:x': 0
'sbg:y': 853.875
- id: biometrics_json
type: boolean?
label: biometrics_json
doc: Also output data in JSON format.
'sbg:x': 0
'sbg:y': 2561.625
- id: biometrics_plot
type: boolean?
label: biometrics_plot
doc: Also output plots of the data.
'sbg:x': 0
'sbg:y': 2454.890625
- id: simplex_bam_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: simplex_bam_pool_a_dir
'sbg:x': 0
'sbg:y': 213.46875
- id: duplex_bam_stats_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: duplex_bam_stats_pool_a_dir
'sbg:x': 0
'sbg:y': 1174.078125
- id: duplex_bam_stats_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: duplex_bam_stats_pool_b_dir
'sbg:x': 0
'sbg:y': 1067.34375
- id: collapsed_bam_stats_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: collapsed_bam_stats_pool_a_dir
'sbg:x': 0
'sbg:y': 2027.953125
- id: collapsed_bam_stats_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: collapsed_bam_stats_pool_b_dir
'sbg:x': 0
'sbg:y': 1921.21875
- id: collapsed_bam_duplex_metrics_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: collapsed_bam_duplex_metrics_pool_a_dir
'sbg:x': 0
'sbg:y': 2241.421875
- id: collapsed_bam_duplex_metrics_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: collapsed_bam_duplex_metrics_pool_b_dir
'sbg:x': 0
'sbg:y': 2134.6875
- id: gatk_mean_quality_by_cycle_recal_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: gatk_mean_quality_by_cycle_recal_dir
'sbg:x': 0
'sbg:y': 320.203125
- id: gatk_mean_quality_by_cycle_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: gatk_mean_quality_by_cycle_dir
'sbg:x': 0
'sbg:y': 426.9375
- id: uncollapsed_bam_stats_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: uncollapsed_bam_stats_pool_b_dir
'sbg:x': 0
'sbg:y': 0
- id: uncollapsed_bam_stats_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: uncollapsed_bam_stats_pool_a_dir
'sbg:x': 0
'sbg:y': 106.734375
- id: biometrics_threads
type: int?
label: biometrics_threads
doc: Number of threads to use.
'sbg:x': 0
'sbg:y': 2348.15625
- id: duplex_biometrics_coverage_threshold
type: int?
label: duplex_biometrics_coverage_threshold
doc: Samples with Y chromosome above this value will be considered male.
'sbg:x': 0
'sbg:y': 960.609375
- id: duplex_biometrics_major_threshold
type: float?
label: duplex_biometrics_major_threshold
doc: Major contamination threshold for bad sample.
'sbg:x': 0
'sbg:y': 747.140625
- id: duplex_biometrics_minor_threshold
type: float?
label: duplex_biometrics_minor_threshold
doc: Minor contamination threshold for bad sample.
'sbg:x': 0
'sbg:y': 640.40625
- id: collapsed_extraction_files
type:
type: array
items: File
inputBinding:
position: 0
prefix: '--input'
label: collapsed_extraction_files
doc: >-
Can be one of three types: (1) path to a CSV file containing sample
information (one per line). For example:
sample_name,sample_bam,sample_type,sample_sex,sample_group. (2) Path to a
'*.pk' file that was produced by the 'extract' tool. (3) Name of the
sample to analyze; this assumes there is a file named '{sample_name}.pk'
in your database directory. Can be specified more than once.
'sbg:x': 0
'sbg:y': 1387.546875
- id: collapsed_biometrics_discordance_threshold
type: float?
label: collapsed_biometrics_discordance_threshold
doc: >-
Discordance values less than this are regarded as matching samples.
(default: 0.05)
'sbg:x': 0
'sbg:y': 1707.75
- id: collapsed_biometrics_major_threshold
type: float?
label: collapsed_biometrics_major_threshold
doc: Major contamination threshold for bad sample.
'sbg:x': 0
'sbg:y': 1601.015625
- id: collapsed_biometrics_minor_threshold
type: float?
label: collapsed_biometrics_minor_threshold
doc: Minor contamination threshold for bad sample.
'sbg:x': 0
'sbg:y': 1494.28125
- id: collapsed_biometrics_coverage_threshold
type: int?
label: collapsed_biometrics_coverage_threshold
doc: Samples with Y chromosome above this value will be considered male.
'sbg:x': 0
'sbg:y': 1814.484375
- id: duplex_bam_sequence_qc_dir
type:
type: array
items:
- File
- Directory
- 'null'
'sbg:x': 0
'sbg:y': 1280.8125
outputs:
- id: simplex_bam_pool_a_outdir
outputSource:
- aggregate/directory
type: Directory
label: simplex_bam_pool_a_outdir
'sbg:x': 887.6491088867188
'sbg:y': 800.5078125
- id: duplex_bam_sequence_qc_outdir
outputSource:
- aggregate/directory
type: Directory
label: duplex_bam_sequence_qc_outdir
'sbg:x': 887.6491088867188
'sbg:y': 1440.9140625
- id: duplex_bam_stats_pool_a_outdir
outputSource:
- aggregate/directory
type: Directory
label: duplex_bam_stats_pool_a_outdir
'sbg:x': 887.6491088867188
'sbg:y': 1334.1796875
- id: duplex_bam_stats_pool_b_outdir
outputSource:
- aggregate/directory
type: Directory
label: duplex_bam_stats_pool_b_outdir
'sbg:x': 887.6491088867188
'sbg:y': 1227.4453125
- id: collapsed_bam_stats_pool_a_outdir
outputSource:
- aggregate/directory
type: Directory
label: collapsed_bam_stats_pool_a_outdir
'sbg:x': 887.6491088867188
'sbg:y': 1761.1171875
- id: collapsed_bam_stats_pool_b_outdir
outputSource:
- aggregate/directory
type: Directory
label: collapsed_bam_stats_pool_b_outdir
'sbg:x': 887.6491088867188
'sbg:y': 1654.3828125
- id: collapsed_bam_duplex_metrics_pool_a_outdir
outputSource:
- aggregate/directory
type: Directory
label: collapsed_bam_duplex_metrics_pool_a_outdir
'sbg:x': 887.6491088867188
'sbg:y': 1974.5859375
- id: collapsed_bam_duplex_metrics_pool_b_outdir
outputSource:
- aggregate/directory
type: Directory
label: collapsed_bam_duplex_metrics_pool_b_outdir
'sbg:x': 887.6491088867188
'sbg:y': 1867.8515625
- id: gatk_mean_quality_by_cycle_outdir
outputSource:
- aggregate/directory
type: Directory
label: gatk_mean_quality_by_cycle_outdir
'sbg:x': 887.6491088867188
'sbg:y': 1013.9765625
- id: uncollapsed_bam_stats_pool_b_outdir
outputSource:
- aggregate/directory
type: Directory
label: uncollapsed_bam_stats_pool_b_outdir
'sbg:x': 887.6491088867188
'sbg:y': 587.0390625
- id: uncollapsed_bam_stats_pool_a_outdir
outputSource:
- aggregate/directory
type: Directory
label: uncollapsed_bam_stats_pool_a_outdir
'sbg:x': 887.6491088867188
'sbg:y': 693.7734375
- id: duplex_biometrics_outdir
outputSource:
- duplex_biometrics_agg/directory
type: Directory
label: duplex_biometrics_outdir
'sbg:x': 1310.180419921875
'sbg:y': 1227.4453125
- id: collapsed_biometrics_outdir
outputSource:
- collapsed_biometrics_agg/directory
type: Directory
label: collapsed_biometrics_outdir
'sbg:x': 1310.180419921875
'sbg:y': 1334.1796875
- id: gatk_mean_quality_by_cycle_recal_outdir
outputSource:
- aggregate/directory
type: Directory
'sbg:x': 887.6491088867188
'sbg:y': 907.2421875
steps:
- id: duplex_biometrics_genotype
in:
- id: input
source:
- duplex_extraction_files
- id: discordance_threshold
source: duplex_biometrics_discordance_threshold
- id: plot
default: true
source: biometrics_plot
- id: json
default: true
source: biometrics_json
- id: threads
source: biometrics_threads
out:
- id: biometrics_genotype_comparisons
- id: biometrics_genotype_cluster_input
- id: biometrics_genotype_cluster_input_database
- id: biometrics_genotype_plot_input
- id: biometrics_genotype_plot_input_database
run: ../command_line_tools/biometrics_genotype/0.2.9/biometrics_genotype.cwl
'sbg:x': 410.1875
'sbg:y': 1245.8125
- id: aggregate
in:
- id: files
linkMerge: merge_flattened
source:
- simplex_bam_pool_a_dir
- duplex_bam_stats_pool_a_dir
- duplex_bam_stats_pool_b_dir
- collapsed_bam_stats_pool_a_dir
- collapsed_bam_stats_pool_b_dir
- collapsed_bam_duplex_metrics_pool_a_dir
- collapsed_bam_duplex_metrics_pool_b_dir
- gatk_mean_quality_by_cycle_recal_dir
- gatk_mean_quality_by_cycle_dir
- uncollapsed_bam_stats_pool_b_dir
- uncollapsed_bam_stats_pool_a_dir
- duplex_bam_sequence_qc_dir
out:
- id: directory
run: ../command_line_tools/expression_tools/put_in_dir.cwl
label: aggregate
scatter:
- files
scatterMethod: dotproduct
'sbg:x': 410
'sbg:y': 487.2613830566406
- id: duplex_biometrics_major
in:
- id: input
source:
- duplex_extraction_files
- id: major_threshold
source: duplex_biometrics_major_threshold
- id: plot
default: true
source: biometrics_plot
- id: json
default: true
source: biometrics_json
out:
- id: biometrics_major_csv
- id: biometrics_major_json
- id: biometrics_major_plot
run: ../command_line_tools/biometrics_major/0.2.9/biometrics_major.cwl
label: duplex_biometrics_major
'sbg:x': 410.1875
'sbg:y': 1090.078125
- id: duplex_biometrics_minor
in:
- id: input
source:
- duplex_extraction_files
- id: minor_threshold
source: duplex_biometrics_minor_threshold
- id: plot
default: true
source: biometrics_plot
- id: json
default: true
source: biometrics_json
out:
- id: biometrics_minor_csv
- id: biometrics_minor_json
- id: biometrics_minor_plot
- id: biometrics_minor_sites_plot
run: ../command_line_tools/biometrics_minor/0.2.9/biometrics_minor.cwl
label: duplex_biometrics_minor
'sbg:x': 410.1875
'sbg:y': 941.34375
- id: duplex_biometrics_sexmismatch
in:
- id: input
source:
- duplex_extraction_files
- id: coverage_threshold
source: duplex_biometrics_coverage_threshold
- id: json
default: true
out:
- id: biometrics_sexmismatch_csv
- id: biometrics_sexmismatch_json
run: >-
../command_line_tools/biometrics_sexmismatch/0.2.9/biometrics_sexmismatch.cwl
label: duplex_biometrics_sexmismatch
'sbg:x': 410.1875
'sbg:y': 806.609375
- id: duplex_biometrics_agg
in:
- id: files
source:
- duplex_biometrics_genotype/biometrics_genotype_plot_input_database
- duplex_biometrics_genotype/biometrics_genotype_plot_input
- duplex_biometrics_genotype/biometrics_genotype_comparisons
- >-
duplex_biometrics_genotype/biometrics_genotype_cluster_input_database
- duplex_biometrics_genotype/biometrics_genotype_cluster_input
- duplex_biometrics_major/biometrics_major_plot
- duplex_biometrics_major/biometrics_major_json
- duplex_biometrics_major/biometrics_major_csv
- duplex_biometrics_minor/biometrics_minor_sites_plot
- duplex_biometrics_minor/biometrics_minor_plot
- duplex_biometrics_minor/biometrics_minor_json
- duplex_biometrics_minor/biometrics_minor_csv
- duplex_biometrics_sexmismatch/biometrics_sexmismatch_json
- duplex_biometrics_sexmismatch/biometrics_sexmismatch_csv
- id: output_directory_name
default: duplex_biometrics_output
out:
- id: directory
run: ../command_line_tools/expression_tools/put_in_dir.cwl
label: duplex_biometrics_agg
'sbg:x': 887.6491088867188
'sbg:y': 1120.7109375
- id: collapsed_biometrics_genotype
in:
- id: input
source:
- collapsed_extraction_files
- id: discordance_threshold
source: collapsed_biometrics_discordance_threshold
- id: plot
default: true
source: biometrics_plot
- id: json
default: true
source: biometrics_json
- id: threads
source: biometrics_threads
out:
- id: biometrics_genotype_comparisons
- id: biometrics_genotype_cluster_input
- id: biometrics_genotype_cluster_input_database
- id: biometrics_genotype_plot_input
- id: biometrics_genotype_plot_input_database
run: ../command_line_tools/biometrics_genotype/0.2.9/biometrics_genotype.cwl
label: collapsed_biometrics_genotype
'sbg:x': 410.1875
'sbg:y': 1840.75
- id: collapsed_biometrics_major
in:
- id: input
source:
- collapsed_extraction_files
- id: major_threshold
default: 0.6
source: collapsed_biometrics_major_threshold
- id: plot
default: true
source: biometrics_plot
- id: json
default: true
source: biometrics_json
out:
- id: biometrics_major_csv
- id: biometrics_major_json
- id: biometrics_major_plot
run: ../command_line_tools/biometrics_major/0.2.9/biometrics_major.cwl
label: collapsed_biometrics_major
'sbg:x': 410.1875
'sbg:y': 1685.015625
- id: collapsed_biometrics_minor
in:
- id: input
source:
- collapsed_extraction_files
- id: minor_threshold
default: 0.002
source: collapsed_biometrics_minor_threshold
- id: plot
default: true
source: biometrics_plot
- id: json
default: true
source: biometrics_json
- id: no_db_comparison
default: false
out:
- id: biometrics_minor_csv
- id: biometrics_minor_json
- id: biometrics_minor_plot
- id: biometrics_minor_sites_plot
run: ../command_line_tools/biometrics_minor/0.2.9/biometrics_minor.cwl
label: collapsed_biometrics_minor
'sbg:x': 410.1875
'sbg:y': 1536.28125
- id: collapsed_biometrics_sexmismatch
in:
- id: input
source:
- collapsed_extraction_files
- id: coverage_threshold
source: collapsed_biometrics_coverage_threshold
- id: json
default: true
source: biometrics_json
out:
- id: biometrics_sexmismatch_csv
- id: biometrics_sexmismatch_json
run: >-
../command_line_tools/biometrics_sexmismatch/0.2.9/biometrics_sexmismatch.cwl
label: collapsed_biometrics_sexmismatch
'sbg:x': 410.1875
'sbg:y': 1394.546875
- id: collapsed_biometrics_agg
in:
- id: files
source:
- >-
collapsed_biometrics_genotype/biometrics_genotype_plot_input_database
- collapsed_biometrics_genotype/biometrics_genotype_plot_input
- collapsed_biometrics_genotype/biometrics_genotype_comparisons
- >-
collapsed_biometrics_genotype/biometrics_genotype_cluster_input_database
- collapsed_biometrics_genotype/biometrics_genotype_cluster_input
- collapsed_biometrics_major/biometrics_major_plot
- collapsed_biometrics_major/biometrics_major_json
- collapsed_biometrics_major/biometrics_major_csv
- collapsed_biometrics_minor/biometrics_minor_sites_plot
- collapsed_biometrics_minor/biometrics_minor_plot
- collapsed_biometrics_minor/biometrics_minor_json
- collapsed_biometrics_minor/biometrics_minor_csv
- collapsed_biometrics_sexmismatch/biometrics_sexmismatch_json
- collapsed_biometrics_sexmismatch/biometrics_sexmismatch_csv
- id: output_directory_name
default: collapsed_biometrics_output
out:
- id: directory
run: ../command_line_tools/expression_tools/put_in_dir.cwl
label: collapsed_biometrics_agg
'sbg:x': 887.6491088867188
'sbg:y': 1547.6484375
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
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