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aggregate_visualize__packed.cwl
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aggregate_visualize__packed.cwl
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{
"$graph": [
{
"class": "Workflow",
"id": "#main",
"label": "aggregate_visualize",
"inputs": [
{
"id": "#duplex_extraction_files",
"type": {
"type": "array",
"items": "File"
}
},
{
"id": "#collapsed_extraction_files",
"type": {
"type": "array",
"items": "File"
}
},
{
"id": "#uncollapsed_bam_stats_pool_a_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#simplex_bam_pool_b_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#simplex_bam_pool_a_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#gatk_mean_quality_by_cycle_recal_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#duplex_bam_stats_pool_b_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#duplex_bam_stats_pool_a_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#collapsed_bam_stats_pool_b_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#collapsed_bam_stats_pool_a_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#collapsed_bam_duplex_metrics_pool_b_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#collapsed_bam_duplex_metrics_pool_a_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#samples-json",
"type": "File"
},
{
"id": "#config",
"type": [
"null",
"File"
]
},
{
"id": "#duplex_bam_sequence_qc_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
},
{
"id": "#uncollapsed_bam_stats_pool_b_dir",
"type": {
"type": "array",
"items": [
"File",
"Directory",
"null"
]
}
}
],
"outputs": [
{
"id": "#multiqc_zip",
"outputSource": [
"#multiqc_1_10_1/multiqc_zip"
],
"type": [
"null",
"File"
]
},
{
"id": "#multiqc_html",
"outputSource": [
"#multiqc_1_10_1/multiqc_html"
],
"type": "File"
},
{
"id": "#multiqc_output_dir",
"outputSource": [
"#multiqc_1_10_1/multiqc_output_dir"
],
"type": "Directory"
}
],
"steps": [
{
"id": "#qc_aggregator",
"in": [
{
"id": "#qc_aggregator/duplex_extraction_files",
"source": [
"#duplex_extraction_files"
]
},
{
"id": "#qc_aggregator/simplex_bam_pool_a_dir",
"source": [
"#simplex_bam_pool_a_dir"
]
},
{
"id": "#qc_aggregator/simplex_bam_pool_b_dir",
"source": [
"#simplex_bam_pool_b_dir"
]
},
{
"id": "#qc_aggregator/duplex_bam_sequence_qc_dir",
"source": [
"#duplex_bam_sequence_qc_dir"
]
},
{
"id": "#qc_aggregator/duplex_bam_stats_pool_a_dir",
"source": [
"#duplex_bam_stats_pool_a_dir"
]
},
{
"id": "#qc_aggregator/duplex_bam_stats_pool_b_dir",
"source": [
"#duplex_bam_stats_pool_b_dir"
]
},
{
"id": "#qc_aggregator/collapsed_bam_stats_pool_a_dir",
"source": [
"#collapsed_bam_stats_pool_a_dir"
]
},
{
"id": "#qc_aggregator/collapsed_bam_stats_pool_b_dir",
"source": [
"#collapsed_bam_stats_pool_b_dir"
]
},
{
"id": "#qc_aggregator/collapsed_bam_duplex_metrics_pool_a_dir",
"source": [
"#collapsed_bam_duplex_metrics_pool_a_dir"
]
},
{
"id": "#qc_aggregator/collapsed_bam_duplex_metrics_pool_b_dir",
"source": [
"#collapsed_bam_duplex_metrics_pool_b_dir"
]
},
{
"id": "#qc_aggregator/gatk_mean_quality_by_cycle_recal_dir",
"source": [
"#gatk_mean_quality_by_cycle_recal_dir"
]
},
{
"id": "#qc_aggregator/uncollapsed_bam_stats_pool_b_dir",
"source": [
"#uncollapsed_bam_stats_pool_b_dir"
]
},
{
"id": "#qc_aggregator/uncollapsed_bam_stats_pool_a_dir",
"source": [
"#uncollapsed_bam_stats_pool_a_dir"
]
},
{
"id": "#qc_aggregator/collapsed_extraction_files",
"source": [
"#collapsed_extraction_files"
]
}
],
"out": [
{
"id": "#qc_aggregator/aggregate_qc_stats"
}
],
"run": "#qc_aggregator.cwl",
"label": "qc_aggregator"
},
{
"id": "#general_stats_parse",
"in": [
{
"id": "#general_stats_parse/directory",
"source": "#qc_aggregator/aggregate_qc_stats"
},
{
"id": "#general_stats_parse/samples-json",
"source": "#samples-json"
},
{
"id": "#general_stats_parse/config",
"source": "#config"
}
],
"out": [
{
"id": "#general_stats_parse/aggregate_parsed_stats"
}
],
"run": "#general_stats_parse.cwl",
"label": "general_stats_parse"
},
{
"id": "#multiqc_1_10_1",
"in": [
{
"id": "#multiqc_1_10_1/qc_files_dir",
"source": "#general_stats_parse/aggregate_parsed_stats"
},
{
"id": "#multiqc_1_10_1/config",
"source": "#config"
}
],
"out": [
{
"id": "#multiqc_1_10_1/multiqc_output_dir"
},
{
"id": "#multiqc_1_10_1/multiqc_html"
},
{
"id": "#multiqc_1_10_1/multiqc_zip"
}
],
"run": "#multiqc.cwl"
}
],
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"$namespaces": {
"sbg": "https://www.sevenbridges.com/"
}
},
{
"class": "CommandLineTool",
"id": "#general_stats_parse.cwl",
"baseCommand": [
"general_stats_parse.py"
],
"arguments": [
"--dir",
"."
],
"inputs": [
{
"id": "#general_stats_parse.cwl/directory",
"type": "Directory",
"doc": "Directory containing results."
},
{
"id": "#general_stats_parse.cwl/samples-json",
"type": "File",
"inputBinding": {
"prefix": "--samples-json"
},
"doc": "Sample JSON file."
},
{
"id": "#general_stats_parse.cwl/config",
"type": [
"null",
"File"
],
"inputBinding": {
"prefix": "--config"
},
"doc": "MultQC config file."
}
],
"outputs": [
{
"id": "#general_stats_parse.cwl/aggregate_parsed_stats",
"label": "aggregate_parsed_stats",
"type": "Directory",
"outputBinding": {
"glob": ".",
"outputEval": "${\n self[0].basename = \"aggregate_qc_stats\";\n return self[0]\n}"
}
}
],
"label": "general_stats_parse",
"requirements": [
{
"class": "DockerRequirement",
"dockerPull": "ghcr.io/msk-access/access_utils:0.1.1"
},
{
"class": "InitialWorkDirRequirement",
"listing": [
{
"entry": "$(inputs.directory)",
"writable": true
}
]
},
{
"class": "InlineJavascriptRequirement"
}
],
"http://purl.org/dc/terms/contributor": [
{
"class": "http://xmlns.com/foaf/0.1/Organization",
"http://xmlns.com/foaf/0.1/member": [
{
"class": "http://xmlns.com/foaf/0.1/Person",
"http://xmlns.com/foaf/0.1/mbox": "mailto:[email protected]",
"http://xmlns.com/foaf/0.1/name": "Ian Johnson"
}
],
"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
}
],
"http://purl.org/dc/terms/creator": [
{
"class": "http://xmlns.com/foaf/0.1/Organization",
"http://xmlns.com/foaf/0.1/member": [
{
"class": "http://xmlns.com/foaf/0.1/Person",
"http://xmlns.com/foaf/0.1/mbox": "mailto:[email protected]",
"http://xmlns.com/foaf/0.1/name": "Ian Johnson"
}
],
"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
}
]
},
{
"class": "CommandLineTool",
"id": "#biometrics_genotype.cwl",
"baseCommand": [
"biometrics",
"genotype"
],
"inputs": [
{
"id": "#biometrics_genotype.cwl/input",
"type": {
"type": "array",
"items": "File",
"inputBinding": {
"position": 0,
"prefix": "--input"
}
},
"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."
},
{
"id": "#biometrics_genotype.cwl/database",
"type": [
"null",
"string"
],
"inputBinding": {
"position": 0,
"prefix": "--database"
},
"doc": "Directory to store the intermediate files after running the extraction step."
},
{
"default": 0.05,
"id": "#biometrics_genotype.cwl/discordance_threshold",
"type": [
"null",
"float"
],
"inputBinding": {
"position": 0,
"prefix": "--discordance-threshold"
},
"doc": "Discordance values less than this are regarded as matching samples. (default: 0.05)"
},
{
"id": "#biometrics_genotype.cwl/prefix",
"type": [
"null",
"string"
],
"inputBinding": {
"position": 0,
"prefix": "--prefix"
},
"doc": "Output file prefix."
},
{
"id": "#biometrics_genotype.cwl/plot",
"type": [
"null",
"boolean"
],
"inputBinding": {
"position": 0,
"prefix": "--plot"
},
"doc": "Also output plots of the data."
},
{
"id": "#biometrics_genotype.cwl/json",
"type": [
"null",
"boolean"
],
"inputBinding": {
"position": 0,
"prefix": "--json"
},
"doc": "Also output data in JSON format."
},
{
"id": "#biometrics_genotype.cwl/no_db_comparison",
"type": [
"null",
"boolean"
],
"inputBinding": {
"position": 0,
"prefix": "--no-db-compare"
},
"doc": "Do not compare the sample(s) you provided to all samples in the database, only compare them with each other."
},
{
"default": 2,
"id": "#biometrics_genotype.cwl/threads",
"type": [
"null",
"int"
],
"inputBinding": {
"position": 0,
"prefix": "--threads"
},
"doc": "Number of threads to use."
}
],
"outputs": [
{
"id": "#biometrics_genotype.cwl/biometrics_genotype_comparisons",
"type": "File",
"outputBinding": {
"glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_genotype_comparison.csv'\n } else {\n return 'genotype_comparison.csv'\n }\n}"
}
},
{
"id": "#biometrics_genotype.cwl/biometrics_genotype_cluster_input",
"type": "File",
"outputBinding": {
"glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_genotype_clusters_input.csv'\n } else {\n return 'genotype_clusters_input.csv'\n }\n}"
}
},
{
"id": "#biometrics_genotype.cwl/biometrics_genotype_cluster_input_database",
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_genotype_clusters_database.csv'\n } else {\n return 'genotype_clusters_database.csv'\n }\n}"
}
},
{
"id": "#biometrics_genotype.cwl/biometrics_genotype_plot_input",
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "${\n return 'genotype_comparison_input.html'\n}"
}
},
{
"id": "#biometrics_genotype.cwl/biometrics_genotype_plot_input_database",
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "${\n return 'genotype_comparison_database.html'\n}"
}
}
],
"requirements": [
{
"class": "ResourceRequirement",
"ramMin": 16000,
"coresMin": 2
},
{
"class": "DockerRequirement",
"dockerPull": "ghcr.io/msk-access/biometrics:0.2.13"
},
{
"class": "InlineJavascriptRequirement"
}
],
"http://purl.org/dc/terms/contributor": [
{
"class": "http://xmlns.com/foaf/0.1/Organization",
"http://xmlns.com/foaf/0.1/member": [
{
"class": "http://xmlns.com/foaf/0.1/Person",
"http://xmlns.com/foaf/0.1/mbox": "mailto:[email protected]",
"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
}
],
"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
}
],
"http://purl.org/dc/terms/creator": [
{
"class": "http://xmlns.com/foaf/0.1/Organization",
"http://xmlns.com/foaf/0.1/member": [
{
"class": "http://xmlns.com/foaf/0.1/Person",
"http://xmlns.com/foaf/0.1/mbox": "mailto:[email protected]",
"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
}
],
"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
}
],
"http://usefulinc.com/ns/doap#release": [
{
"class": "http://usefulinc.com/ns/doap#Version",
"http://usefulinc.com/ns/doap#name": "biometrics",
"http://usefulinc.com/ns/doap#revision": "0.2.13"
}
]
},
{
"class": "CommandLineTool",
"id": "#biometrics_major.cwl",
"baseCommand": [
"biometrics",
"major"
],
"inputs": [
{
"id": "#biometrics_major.cwl/input",
"type": {
"type": "array",
"items": "File",
"inputBinding": {
"prefix": "--input"
}
},
"inputBinding": {
"position": 0
},
"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."
},
{
"id": "#biometrics_major.cwl/database",
"type": [
"null",
"string"
],
"inputBinding": {
"position": 0,
"prefix": "--database"
},
"doc": "Directory to store the intermediate files after running the extraction step."
},
{
"default": 0.6,
"id": "#biometrics_major.cwl/major_threshold",
"type": [
"null",
"float"
],
"inputBinding": {
"position": 0,
"prefix": "--major-threshold"
},
"doc": "Major contamination threshold for bad sample."
},
{
"id": "#biometrics_major.cwl/prefix",
"type": [
"null",
"string"
],
"inputBinding": {
"position": 0,
"prefix": "--prefix"
},
"doc": "Output file prefix."
},
{
"id": "#biometrics_major.cwl/plot",
"type": [
"null",
"boolean"
],
"inputBinding": {
"position": 0,
"prefix": "--plot"
},
"doc": "Also output plots of the data."
},
{
"id": "#biometrics_major.cwl/json",
"type": [
"null",
"boolean"
],
"inputBinding": {
"position": 0,
"prefix": "--json"
},
"doc": "Also output data in JSON format."
},
{
"id": "#biometrics_major.cwl/no_db_comparison",
"type": [
"null",
"boolean"
],
"inputBinding": {
"position": 0,
"prefix": "--no-db-compare"
},
"doc": "Do not compare the sample(s) you provided to all samples in the database, only compare them with each other."
}
],
"outputs": [
{
"id": "#biometrics_major.cwl/biometrics_major_csv",
"type": "File",
"outputBinding": {
"glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_major_contamination.csv'\n } else {\n return 'major_contamination.csv'\n }\n}"
}
},
{
"id": "#biometrics_major.cwl/biometrics_major_json",
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_major_contamination.json'\n } else {\n return 'major_contamination.json'\n }\n}"
}
},
{
"id": "#biometrics_major.cwl/biometrics_major_plot",
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "${\n return 'major_contamination.html'\n}"
}
}
],
"requirements": [
{
"class": "ResourceRequirement",
"ramMin": 16000,
"coresMin": 2
},
{
"class": "DockerRequirement",
"dockerPull": "ghcr.io/msk-access/biometrics:0.2.13"
},
{
"class": "InlineJavascriptRequirement"
}
],
"http://purl.org/dc/terms/contributor": [
{
"class": "http://xmlns.com/foaf/0.1/Organization",
"http://xmlns.com/foaf/0.1/member": [
{
"class": "http://xmlns.com/foaf/0.1/Person",
"http://xmlns.com/foaf/0.1/mbox": "mailto:[email protected]",
"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
}
],
"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
}
],
"http://purl.org/dc/terms/creator": [
{
"class": "http://xmlns.com/foaf/0.1/Organization",
"http://xmlns.com/foaf/0.1/member": [
{
"class": "http://xmlns.com/foaf/0.1/Person",
"http://xmlns.com/foaf/0.1/mbox": "mailto:[email protected]",
"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
}
],
"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
}
],
"http://usefulinc.com/ns/doap#release": [
{
"class": "http://usefulinc.com/ns/doap#Version",
"http://usefulinc.com/ns/doap#name": "biometrics",
"http://usefulinc.com/ns/doap#revision": "0.2.13"
}
]
},
{
"class": "CommandLineTool",
"id": "#biometrics_minor.cwl",
"baseCommand": [
"biometrics",
"minor"
],
"inputs": [
{
"id": "#biometrics_minor.cwl/input",
"type": {
"type": "array",
"items": "File",
"inputBinding": {
"prefix": "--input"
}
},
"inputBinding": {
"position": 0
},
"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."
},
{
"id": "#biometrics_minor.cwl/database",
"type": [
"null",
"string"
],
"inputBinding": {
"position": 0,
"prefix": "--database"
},
"doc": "Directory to store the intermediate files after running the extraction step."
},
{
"default": 0.002,
"id": "#biometrics_minor.cwl/minor_threshold",
"type": [
"null",
"float"
],
"inputBinding": {
"position": 0,
"prefix": "--minor-threshold"
},
"doc": "Minor contamination threshold for bad sample."
},
{
"id": "#biometrics_minor.cwl/prefix",
"type": [
"null",
"string"
],
"inputBinding": {
"position": 0,
"prefix": "--prefix"
},
"doc": "Output file prefix."
},
{
"id": "#biometrics_minor.cwl/plot",
"type": [
"null",
"boolean"
],
"inputBinding": {
"position": 0,
"prefix": "--plot"
},
"doc": "Also output plots of the data."
},
{
"id": "#biometrics_minor.cwl/json",
"type": [
"null",
"boolean"
],
"inputBinding": {
"position": 0,
"prefix": "--json"
},
"doc": "Also output data in JSON format."
},
{
"id": "#biometrics_minor.cwl/no_db_comparison",
"type": [
"null",
"boolean"
],
"inputBinding": {
"position": 0,
"prefix": "--no-db-compare"
},
"doc": "Do not compare the sample(s) you provided to all samples in the database, only compare them with each other."
}
],
"outputs": [
{
"id": "#biometrics_minor.cwl/biometrics_minor_csv",
"type": "File",
"outputBinding": {
"glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_minor_contamination.csv'\n } else {\n return 'minor_contamination.csv'\n }\n}"
}
},
{
"id": "#biometrics_minor.cwl/biometrics_minor_json",
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_minor_contamination.json'\n } else {\n return 'minor_contamination.json'\n }\n}"
}
},
{
"id": "#biometrics_minor.cwl/biometrics_minor_plot",
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "${\n return 'minor_contamination.html'\n}"
}
},
{
"id": "#biometrics_minor.cwl/biometrics_minor_sites_plot",
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "${\n return 'minor_contamination_sites.html'\n}"
}
}
],
"requirements": [
{
"class": "ResourceRequirement",
"ramMin": 16000,
"coresMin": 2
},
{
"class": "DockerRequirement",
"dockerPull": "ghcr.io/msk-access/biometrics:0.2.13"
},
{
"class": "InlineJavascriptRequirement"
}
],
"http://purl.org/dc/terms/contributor": [
{
"class": "http://xmlns.com/foaf/0.1/Organization",
"http://xmlns.com/foaf/0.1/member": [
{
"class": "http://xmlns.com/foaf/0.1/Person",
"http://xmlns.com/foaf/0.1/mbox": "mailto:[email protected]",
"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
}
],
"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
}
],
"http://purl.org/dc/terms/creator": [
{
"class": "http://xmlns.com/foaf/0.1/Organization",
"http://xmlns.com/foaf/0.1/member": [
{
"class": "http://xmlns.com/foaf/0.1/Person",
"http://xmlns.com/foaf/0.1/mbox": "mailto:[email protected]",
"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
}
],
"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
}
],
"http://usefulinc.com/ns/doap#release": [
{
"class": "http://usefulinc.com/ns/doap#Version",
"http://usefulinc.com/ns/doap#name": "biometrics",
"http://usefulinc.com/ns/doap#revision": "0.2.13"
}
]
},
{
"class": "CommandLineTool",
"id": "#biometrics_sexmismatch.cwl",