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This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -20,27 +20,27 @@ inputs: '*.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 @@ -49,8 +49,18 @@ inputs: - 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 @@ -59,8 +69,8 @@ inputs: - 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 @@ -69,8 +79,8 @@ inputs: - 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 @@ -79,8 +89,8 @@ inputs: - 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 @@ -89,8 +99,8 @@ inputs: - 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 @@ -99,8 +109,8 @@ inputs: - 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 @@ -109,8 +119,8 @@ inputs: - 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 @@ -119,8 +129,8 @@ inputs: - 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 @@ -129,8 +139,8 @@ inputs: - 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 @@ -139,8 +149,8 @@ inputs: - 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 @@ -149,32 +159,32 @@ inputs: - 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 @@ -190,141 +200,56 @@ inputs: '*.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: @@ -348,12 +273,11 @@ steps: - 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 @@ -367,15 +291,28 @@ steps: - 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 @@ -395,8 +332,8 @@ steps: - 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 @@ -417,8 +354,8 @@ steps: - 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 @@ -434,8 +371,8 @@ steps: 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 @@ -461,8 +398,8 @@ steps: - 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 @@ -486,8 +423,8 @@ steps: - 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 @@ -508,8 +445,8 @@ steps: - 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 @@ -533,8 +470,8 @@ steps: - 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 @@ -551,8 +488,8 @@ steps: 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 @@ -579,8 +516,8 @@ steps: - 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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This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,586 @@ 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