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ionox0/access_qc_aggregator.cwl

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access_qc_aggregator.cwl
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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': -432.869140625
'sbg:y': 130.13436889648438
- id: duplex_biometrics_discordance_threshold
type: float?
doc: >-
Discordance values less than this are regarded as matching samples.
(default: 0.05)
'sbg:x': -439.3351745605469
'sbg:y': -10.98059368133545
- id: biometrics_json
type: boolean?
label: biometrics_json
doc: Also output data in JSON format.
'sbg:x': -886.3317260742188
'sbg:y': 1000.4258422851562
- id: biometrics_plot
type: boolean?
label: biometrics_plot
doc: Also output plots of the data.
'sbg:x': -890.3317260742188
'sbg:y': 846.9597778320312
- id: simplex_bam_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: simplex_bam_pool_a_dir
'sbg:x': -373.4821472167969
'sbg:y': -2165.392822265625
- id: duplex_bam_sequence_qc_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: duplex_bam_sequence_qc_dir
'sbg:x': -364.5106506347656
'sbg:y': -2014.1710205078125
- id: duplex_bam_stats_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: duplex_bam_stats_pool_a_dir
'sbg:x': -366.6091613769531
'sbg:y': -1860.9732666015625
- id: duplex_bam_stats_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: duplex_bam_stats_pool_b_dir
'sbg:x': -358.2148742675781
'sbg:y': -1711.974609375
- id: collapsed_bam_stats_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: collapsed_bam_stats_pool_a_dir
'sbg:x': -355.0670166015625
'sbg:y': -1557.7293701171875
- id: collapsed_bam_stats_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: collapsed_bam_stats_pool_b_dir
'sbg:x': -349.820556640625
'sbg:y': -1377.2520751953125
- 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': -346.6726989746094
'sbg:y': -1234.5489501953125
- 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': -336.1798400878906
'sbg:y': -1068.7615966796875
- 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': -334.0812683105469
'sbg:y': -918.7134399414062
- id: gatk_mean_quality_by_cycle_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: gatk_mean_quality_by_cycle_dir
'sbg:x': -342.4755554199219
'sbg:y': -761.3282470703125
- id: uncollapsed_bam_stats_pool_b_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: uncollapsed_bam_stats_pool_b_dir
'sbg:x': -334.0872497558594
'sbg:y': -610.5114135742188
- id: uncollapsed_bam_stats_pool_a_dir
type:
type: array
items:
- File
- Directory
- 'null'
label: uncollapsed_bam_stats_pool_a_dir
'sbg:x': -340.1039123535156
'sbg:y': -475.7384948730469
- id: biometrics_threads
type: int?
label: biometrics_threads
doc: Number of threads to use.
'sbg:x': -882.580322265625
'sbg:y': 707.580322265625
- 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': -415.4972229003906
'sbg:y': 578.8967895507812
- id: duplex_biometrics_major_threshold
type: float?
label: duplex_biometrics_major_threshold
doc: Major contamination threshold for bad sample.
'sbg:x': -424.0810241699219
'sbg:y': 279.0644226074219
- id: duplex_biometrics_minor_threshold
type: float?
label: duplex_biometrics_minor_threshold
doc: Minor contamination threshold for bad sample.
'sbg:x': -412.9134216308594
'sbg:y': 428.7292175292969
- 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': -397.1647033691406
'sbg:y': 933.3253784179688
- 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': -397.409912109375
'sbg:y': 1063.6241455078125
- id: collapsed_biometrics_major_threshold
type: float?
label: collapsed_biometrics_major_threshold
doc: Major contamination threshold for bad sample.
'sbg:x': -385.83941650390625
'sbg:y': 1202.94287109375
- id: collapsed_biometrics_minor_threshold
type: float?
label: collapsed_biometrics_minor_threshold
doc: Minor contamination threshold for bad sample.
'sbg:x': -381.01446533203125
'sbg:y': 1344.0721435546875
- 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': -387.0456237792969
'sbg:y': 1481.5826416015625
outputs:
- id: outdir
outputSource:
- aggregate/directory
type: Directory[]
label: outdir
'sbg:x': 315.71063232421875
'sbg:y': -451.6719055175781
- id: duplex_biometrics_outdir
outputSource:
- duplex_biometrics_agg/directory
type: Directory
label: duplex_biometrics_outdir
'sbg:x': 735.8389282226562
'sbg:y': 382.3530578613281
- id: collapsed_biometrics_outdir
outputSource:
- collapsed_biometrics_agg/directory
type: Directory
label: collapsed_biometrics_outdir
'sbg:x': 855.2215576171875
'sbg:y': 1238.1143798828125
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': 15.982142448425293
'sbg:y': 126.89286041259766
- id: aggregate
in:
- id: files
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
- id: output_directory_name
default:
valueFrom: >-
$([ "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
- output_directory_name
scatterMethod: dotproduct
'sbg:x': -5
'sbg:y': -785
- 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': 19.419479370117188
'sbg:y': 303.0918273925781
- 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': 17.838956832885742
'sbg:y': 492.78192138671875
- 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': 12.246261596679688
'sbg:y': 665.076904296875
- 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': 432.8553466796875
'sbg:y': 381.737060546875
- 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': 30.168201446533203
'sbg:y': 924.2750244140625
- 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': 37.61433792114258
'sbg:y': 1125.25341796875
- 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': 37.22428512573242
'sbg:y': 1325.6654052734375
- 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': 38.33828353881836
'sbg:y': 1529
- 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': 585.7066650390625
'sbg:y': 1235.0516357421875
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
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