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Can be specified more than once." }, { "id": "#biometrics_minor.cwl_2/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_2/minor_threshold", "type": [ "null", "float" ], "inputBinding": { "position": 0, "prefix": "--minor-threshold" }, "doc": "Minor contamination threshold for bad sample." }, { "id": "#biometrics_minor.cwl_2/prefix", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--prefix" }, "doc": "Output file prefix." }, { "id": "#biometrics_minor.cwl_2/plot", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--plot" }, "doc": "Also output plots of the data." }, { "id": "#biometrics_minor.cwl_2/json", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--json" }, "doc": "Also output data in JSON format." }, { "id": "#biometrics_minor.cwl_2/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_2/biometrics_minor_csv", "type": "File", "outputBinding": { "glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_minor_contamination.csv'\n } else {\n return 'minor_contamination.csv'\n }\n}" } }, { "id": "#biometrics_minor.cwl_2/biometrics_minor_json", "type": [ "null", "File" ], "outputBinding": { "glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_minor_contamination.json'\n } else {\n return 'minor_contamination.json'\n }\n}" } }, { "id": "#biometrics_minor.cwl_2/biometrics_minor_plot", "type": [ "null", "File" ], "outputBinding": { "glob": "${\n return 'minor_contamination.html'\n}" } }, { "id": "#biometrics_minor.cwl_2/biometrics_minor_sites_plot", "type": [ "null", "File" ], "outputBinding": { "glob": "${\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:murphyc4@mskcc.org", "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:murphyc4@mskcc.org", "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_2", "baseCommand": [ "biometrics", "sexmismatch" ], "inputs": [ { "id": "#biometrics_sexmismatch.cwl_2/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). 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Can be specified more than once." }, { "id": "#biometrics_sexmismatch.cwl_2/database", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--database" }, "doc": "Directory to store the intermediate files after running the extraction step." }, { "default": 50, "id": "#biometrics_sexmismatch.cwl_2/coverage_threshold", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--coverage-threshold" }, "doc": "Samples with Y chromosome above this value will be considered male." }, { "id": "#biometrics_sexmismatch.cwl_2/prefix", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--prefix" }, "doc": "Output file prefix." }, { "id": "#biometrics_sexmismatch.cwl_2/json", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--json" }, "doc": "Also output data in JSON format." }, { "id": "#biometrics_sexmismatch.cwl_2/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_sexmismatch.cwl_2/biometrics_sexmismatch_csv", "type": "File", "outputBinding": { "glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_sex_mismatch.csv'\n } else {\n return 'sex_mismatch.csv'\n }\n}" } }, { "id": "#biometrics_sexmismatch.cwl_2/biometrics_sexmismatch_json", "type": [ "null", "File" ], "outputBinding": { "glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_sex_mismatch.json'\n } else {\n return 'sex_mismatch.json'\n }\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:murphyc4@mskcc.org", "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:murphyc4@mskcc.org", "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": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl", "baseCommand": [ "fgbio" ], "inputs": [ { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/memory_per_job", "type": [ "null", "int" ], "doc": "Memory per job in megabytes" }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/memory_overhead", "type": [ "null", "int" ], "doc": "Memory overhead per job in megabytes" }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/number_of_threads", "type": [ "null", "int" ] }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/input", "type": "File", "inputBinding": { "position": 2, "prefix": "--input" }, "doc": "Input BAM file generated by GroupReadByUmi." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/output_prefix", "type": [ "null", "string" ], "doc": "Prefix of output files to write." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/intervals", "type": [ "null", "File" ], "inputBinding": { "position": 2, "prefix": "--intervals" }, "doc": "Optional set of intervals over which to restrict analysis. [Optional]." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/description", "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--description" }, "doc": "Description of data set used to label plots. Defaults to sample/library. [Optional]." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/duplex_umi_counts", "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--duplex-umi-counts" }, "doc": "If true, produce the .duplex_umi_counts.txt file with counts of duplex UMI observations. [Optional]." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/min_ab_reads", "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--min-ab-reads" }, "doc": "Minimum AB reads to call a tag family a 'duplex'. [Optional]." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/min_ba_reads", "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--min-ba-reads" }, "doc": "Minimum BA reads to call a tag family a 'duplex'. [Optional]." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/umi_tag", "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--umi-tag" }, "doc": "The tag containing the raw UMI. [Optional]." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/mi_tag", "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--mi-tag" }, "doc": "The output tag for UMI grouping. [Optional]." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/temporary_directory", "type": [ "null", "string" ], "doc": "Default value: null." }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/async_io", "type": [ "null", "string" ], "inputBinding": { "position": 0, "separate": false, "prefix": "--async-io=" }, "doc": "'Use asynchronous I/O where possible, e.g. for SAM and BAM files [=true|false].'" } ], "outputs": [ { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/fgbio_collect_duplex_seq_metrics_family_size", "type": "File", "outputBinding": { "glob": "${\n if(inputs.output_prefix){\n return inputs.output_prefix + '.family_sizes.txt'\n }\n else{\n return inputs.input.basename.replace('.bam','.family_sizes.txt')\n }\n}" } }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/fgbio_collect_duplex_seq_metrics_duplex_family_size", "type": "File", "outputBinding": { "glob": "${\n if(inputs.output_prefix){\n return inputs.output_prefix + '.duplex_family_sizes.txt'\n }\n else{\n return inputs.input.basename.replace('.bam','.duplex_family_sizes.txt')\n }\n}" } }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/fgbio_collect_duplex_seq_metrics_duplex_yield_metrics", "type": "File", "outputBinding": { "glob": "${\n if(inputs.output_prefix){\n return inputs.output_prefix + '.duplex_yield_metrics.txt'\n }\n else{\n return inputs.input.basename.replace('.bam','.duplex_yield_metrics.txt')\n }\n}" } }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/fgbio_collect_duplex_seq_metrics_umi_counts", "type": "File", "outputBinding": { "glob": "${\n if(inputs.output_prefix){\n return inputs.output_prefix + '.umi_counts.txt'\n }\n else{\n return inputs.input.basename.replace('.bam','.umi_counts.txt')\n }\n}" } }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/fgbio_collect_duplex_seq_metrics_duplex_qc", "type": [ "null", "File" ], "outputBinding": { "glob": "${\n if(inputs.output_prefix){\n return inputs.output_prefix + '.duplex_qc.pdf'\n }\n else{\n return inputs.input.basename.replace('.bam','.duplex_qc.pdf')\n }\n}" } }, { "id": "#fgbio_collect_duplex_seq_metrics_1.2.0.cwl/fgbio_collect_duplex_seq_metrics_duplex_umi_counts", "type": [ "null", "File" ], "outputBinding": { "glob": "${\n if (inputs.output_prefix) {\n return inputs.output_prefix + '.duplex_umi_counts.txt'\n } else {\n return inputs.input.basename.replace('.bam','.duplex_umi_counts.txt')\n }\n}" } } ], "doc": "Collects a suite of metrics to QC duplex sequencing data.\nInputs ------\nThe input to this tool must be a BAM file that is either:\n1. The exact BAM output by the 'GroupReadsByUmi' tool (in the sort-order it was produced in) 2. A BAM file that has MI tags present on all reads (usually set by 'GroupReadsByUmi' and has been sorted with\n 'SortBam' into 'TemplateCoordinate' order.\n\nCalculation of metrics may be restricted to a set of regions using the '--intervals' parameter. This can significantly affect results as off-target reads in duplex sequencing experiments often have very different properties than on-target reads due to the lack of enrichment.\nSeveral metrics are calculated related to the fraction of tag families that have duplex coverage. The definition of \"duplex\" is controlled by the '--min-ab-reads' and '--min-ba-reads' parameters. The default is to treat any tag family with at least one observation of each strand as a duplex, but this could be made more stringent, e.g. by setting '--min-ab-reads=3 --min-ba-reads=3'. If different thresholds are used then '--min-ab-reads' must be the higher value.\nOutputs -------\nThe following output files are produced:\n1. .family_sizes.txt: metrics on the frequency of different types of families of different sizes 2. .duplex_family_sizes.txt: metrics on the frequency of duplex tag families by the number of observations\n from each strand\n3. .duplex_yield_metrics.txt: summary QC metrics produced using 5%, 10%, 15%...100% of the data 4. .umi_counts.txt: metrics on the frequency of observations of UMIs within reads and tag families 5. .duplex_qc.pdf: a series of plots generated from the preceding metrics files for visualization 6. .duplex_umi_counts.txt: (optional) metrics on the frequency of observations of duplex UMIs within reads\n and tag families. This file is only produced if the '--duplex-umi-counts' option is used as it requires significantly\n more memory to track all pairs of UMIs seen when a large number of UMI sequences are present.\n\nWithin the metrics files the prefixes 'CS', 'SS' and 'DS' are used to mean:\n* CS: tag families where membership is defined solely on matching genome coordinates and strand * SS: single-stranded tag families where membership is defined by genome coordinates, strand and UMI; ie. 50/A and\n 50/B are considered different tag families.\n* DS: double-stranded tag families where membership is collapsed across single-stranded tag families from the same\n double-stranded source molecule; i.e. 50/A and 50/B become one family\n\nRequirements ------------\nFor plots to be generated R must be installed and the ggplot2 package installed with suggested dependencies. Successfully executing the following in R will ensure a working installation:\ninstall.packages(\"ggplot2\", repos=\"http://cran.us.r-project.org\", dependencies=TRUE)", "label": "fgbio_collect_duplex_seq_metrics_1.2.0", "arguments": [ { "position": 0, "valueFrom": "${\n if(inputs.memory_per_job && inputs.memory_overhead) {\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if (inputs.memory_per_job && !inputs.memory_overhead){\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if(!inputs.memory_per_job && inputs.memory_overhead){\n return \"-Xmx12G\"\n }\n else {\n return \"-Xmx12G\"\n }\n}" }, { "position": 0, "valueFrom": "-XX:-UseGCOverheadLimit" }, { "position": 1, "valueFrom": "CollectDuplexSeqMetrics" }, { "position": 0, "prefix": "--tmp-dir=", "separate": false, "valueFrom": "${\n if(inputs.temporary_directory)\n return inputs.temporary_directory;\n return runtime.tmpdir\n}" }, { "position": 2, "prefix": "--output", "valueFrom": "${\n if(inputs.output_prefix){\n return inputs.output_prefix\n }\n else{\n return inputs.input.basename.replace(/.bam/,'')\n }\n}" } ], "requirements": [ { "class": "ResourceRequirement", "ramMin": 16000, "coresMin": 2 }, { "class": "DockerRequirement", "dockerPull": "ghcr.io/msk-access/fgbio:1.2.0" }, { "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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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": "fgbio CollectDuplexSeqMetrics", "http://usefulinc.com/ns/doap#revision": "1.2.0" } ] }, { "class": "CommandLineTool", "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl", "baseCommand": [ "gatk", "CollectAlignmentSummaryMetrics" ], "inputs": [ { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/memory_per_job", "type": [ "null", "int" ], "doc": "Memory per job in megabytes" }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/memory_overhead", "type": [ "null", "int" ], "doc": "Memory overhead per job in megabytes" }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/number_of_threads", "type": [ "null", "int" ] }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/input", "type": "File", "inputBinding": { "position": 0, "prefix": "-I" }, "doc": "Input file (bam or sam). Required." }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/output_file_name", "type": [ "null", "string" ], "doc": "File to write the output to. Required." }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/reference", "type": [ "null", "File" ], "inputBinding": { "position": 0, "prefix": "-R" }, "doc": "Reference sequence file. Note that while this argument is not required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary. Default value: null.", "secondaryFiles": [ "^.fasta.fai", "^.dict" ] }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/adaptor_sequence", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--ADAPTER_SEQUENCE" }, "doc": "List of adapter sequences to use when processing the alignment metrics. This argument may be specified 0 or more times. Default value: [AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG]." }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/metrics_acciumulation_level", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--METRIC_ACCUMULATION_LEVEL" }, "doc": "The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list." }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/expected_pair_orientations", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--EXPECTED_PAIR_ORIENTATIONS" }, "doc": "Paired-end reads that do not have this expected orientation will be considered chimeric. This argument may be specified 0 or more times. Default value: [FR]. Possible values: {FR, RF, TANDEM}" }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/is_bisulfite_sequenced", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--IS_BISULFITE_SEQUENCED" }, "doc": "Whether the SAM or BAM file consists of bisulfite sequenced reads. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/max_insert_size", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--MAX_INSERT_SIZE" }, "doc": "Paired-end reads above this insert size will be considered chimeric along with inter-chromosomal pairs. Default value: 100000." }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/validation_stringency", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--VALIDATION_STRINGENCY" }, "doc": "Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This option can be set to 'null' to clear the default value. Possible values: {STRICT,LENIENT, SILENT}" }, { "default": true, "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/assume_sorted", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--ASSUME_SORTED" }, "doc": "If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}" }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/stop_after", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--STOP_AFTER" }, "doc": "Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value." }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/create_index", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_INDEX" }, "doc": "Whether to create a BAM index when writing a coordinate-sorted BAM file. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/create_md5_file", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_MD5_FILE" }, "doc": "Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/use_jdk_deflater", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--USE_JDK_DEFLATER" }, "doc": "Use the JDK Deflater instead of the Intel Deflater for writing compressed output" }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/use_jdk_inflater", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--USE_JDK_INFLATER" }, "doc": "Use the JDK Inflater instead of the Intel Inflater for reading compressed input" }, { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/temporary_directory", "type": [ "null", "string" ], "doc": "Default value: null. This option may be specified 0 or more times." } ], "outputs": [ { "id": "#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl/gatk_collect_alignment_summary_metrics_txt", "type": "File", "outputBinding": { "glob": "${\n if (inputs.output_file_name){\n return inputs.output_file_name\n } else {\n return inputs.input.basename.replace(/.bam/, '_alignment_summary_metrics.txt')\n }\n}" } } ], "label": "GATK-CollectAlignmentSummaryMetrics", "arguments": [ { "position": 0, "prefix": "--java-options", "valueFrom": "${\n if(inputs.memory_per_job && inputs.memory_overhead) {\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if (inputs.memory_per_job && !inputs.memory_overhead){\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if(!inputs.memory_per_job && inputs.memory_overhead){\n return \"-Xmx15G\"\n }\n else {\n return \"-Xmx15G\"\n }\n}" }, { "position": 0, "prefix": "--TMP_DIR", "valueFrom": "${\n if(inputs.temporary_directory)\n return inputs.temporary_directory;\n return runtime.tmpdir\n}" }, { "position": 0, "prefix": "-O", "valueFrom": "${\n if(inputs.output_file_name){\n return inputs.output_file_name\n } else {\n return inputs.input.basename.replace(/.bam/, '_alignment_summary_metrics.txt')\n }\n}" } ], "requirements": [ { "class": "ResourceRequirement", "ramMin": 32000, "coresMin": 1 }, { "class": "DockerRequirement", "dockerPull": "ghcr.io/msk-access/gatk:4.1.8.0" }, { "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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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": "gatk4", "http://usefulinc.com/ns/doap#revision": "4.1.8.0" } ] }, { "class": "CommandLineTool", "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl", "baseCommand": [ "gatk", "CollectHsMetrics" ], "inputs": [ { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/input", "type": "File", "inputBinding": { "position": 0, "prefix": "-I" }, "doc": "An aligned SAM or BAM file. Required." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/bait_intervals", "type": "File", "inputBinding": { "position": 0, "prefix": "--BAIT_INTERVALS" }, "doc": "An interval list file that contains the locations of the baits used. This argument must be specified at least once. Required." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/target_intervals", "type": "File", "inputBinding": { "position": 0, "prefix": "--TARGET_INTERVALS" }, "doc": "An interval list file that contains the locations of the targets. This argument must be specified at least once. Required." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/output_file_name", "type": [ "null", "string" ], "doc": "The output file to write the metrics to. Required." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/per_base_coverage", "type": [ "null", "string" ], "doc": "An optional file to output per base coverage information to. The per-base file contains one line per target base and can grow very large. It is not recommended for use with large target sets. Default value: null." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/per_target_coverage", "type": [ "null", "string" ], "doc": "An optional file to output per target coverage information to. Default value: null." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/theoretical_sensitivity_output", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--THEORETICAL_SENSITIVITY_OUTPUT" }, "doc": "Output for Theoretical Sensitivity metrics where the allele fractions are provided by the ALLELE_FRACTION argument. Default value: null." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/allele_fraction", "type": [ "null", "float" ], "inputBinding": { "position": 0, "prefix": "--ALLELE_FRACTION" }, "doc": "Allele fraction for which to calculate theoretical sensitivity. This argument may be specified 0 or more times. Default value: [0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5]." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/bait_set_name", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--BAIT_SET_NAME" }, "doc": "Bait set name. If not provided it is inferred from the filename of the bait intervals. Default value: null." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/clip_overlapping_reads", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CLIP_OVERLAPPING_READS" }, "doc": "True if we are to clip overlapping reads, false otherwise. Default value: true. Possible values: {true, false}" }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/coverage_cap", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--COVERAGE_CAP" }, "doc": "Parameter to set a max coverage limit for Theoretical Sensitivity calculations. Default is 200. Default value: 200." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/include_indels", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--INCLUDE_INDELS" }, "doc": "If true count inserted bases as on target and deleted bases as covered by a read. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/minimum_base_quality", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--MINIMUM_BASE_QUALITY" }, "doc": "Minimum base quality for a base to contribute coverage. Default value: 20." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/minimum_mapping_quality", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--MINIMUM_MAPPING_QUALITY" }, "doc": "Minimum mapping quality for a read to contribute coverage. Default value: 20." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/near_distance", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--NEAR_DISTANCE" }, "doc": "The maximum distance between a read and the nearest probe/bait/amplicon for the read to be considered 'near probe' and included in percent selected. Default value: 250." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/sample_size", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--SAMPLE_SIZE" }, "doc": "Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000. Default value: 10000." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/reference", "type": [ "null", "File" ], "inputBinding": { "position": 0, "prefix": "-R" }, "doc": "Reference sequence file. Note that while this argument is not required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary. Default value: null.", "secondaryFiles": [ "^.fasta.fai", "^.dict" ] }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/metrics_acciumulation_level", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--METRIC_ACCUMULATION_LEVEL" }, "doc": "The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list." }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/validation_stringency", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--VALIDATION_STRINGENCY" }, "doc": "Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This option can be set to 'null' to clear the default value. Possible values: {STRICT,LENIENT, SILENT}" }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/create_index", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_INDEX" }, "doc": "Whether to create a BAM index when writing a coordinate-sorted BAM file. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/create_md5_file", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_MD5_FILE" }, "doc": "Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/memory_per_job", "type": [ "null", "int" ], "doc": "Memory per job in megabytes" }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/memory_overhead", "type": [ "null", "int" ], "doc": "Memory overhead per job in megabytes" }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/number_of_threads", "type": [ "null", "int" ] }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/temporary_directory", "type": [ "null", "string" ], "doc": "Default value: null. This option may be specified 0 or more times." } ], "outputs": [ { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/gatk_collect_hs_metrics_txt", "type": "File", "outputBinding": { "glob": "${\n if(inputs.output_file_name){\n return inputs.output_file_name\n } else {\n return inputs.input.basename.replace(/.bam/, '_hs_metrics.txt')\n }\n}" } }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/gatk_collect_hs_metrics_per_base_coverage_txt", "type": "File", "outputBinding": { "glob": "${\n if(inputs.per_base_coverage){\n return inputs.per_base_coverage\n } else {\n return inputs.input.basename.replace(/.bam/, '_per_base_coverage.txt')\n }\n}" } }, { "id": "#gatk_collect_hs_metrics_4.1.8.0.cwl/gatk_collect_hs_metrics_per_target_coverage_txt", "type": "File", "outputBinding": { "glob": "${\n if(inputs.per_target_coverage){\n return inputs.per_target_coverage\n } else {\n return inputs.input.basename.replace(/.bam/, '_per_target_coverage.txt')\n }\n}" } } ], "label": "GATK-CollectHsMetrics", "arguments": [ { "position": 0, "prefix": "--java-options", "valueFrom": "${\n if(inputs.memory_per_job && inputs.memory_overhead) {\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if (inputs.memory_per_job && !inputs.memory_overhead){\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if(!inputs.memory_per_job && inputs.memory_overhead){\n return \"-Xmx15G\"\n }\n else {\n return \"-Xmx15G\"\n }\n}" }, { "position": 0, "prefix": "--TMP_DIR", "valueFrom": "${\n if(inputs.temporary_directory)\n return inputs.temporary_directory;\n return runtime.tmpdir\n}" }, { "position": 0, "prefix": "-O", "valueFrom": "${\n if(inputs.output_file_name){\n return inputs.output_file_name\n } else {\n return inputs.input.basename.replace(/.bam/, '_hs_metrics.txt')\n }\n}" }, { "position": 0, "prefix": "--PER_TARGET_COVERAGE", "valueFrom": "${\n if(inputs.per_target_coverage){\n return inputs.per_target_coverage\n } else {\n return inputs.input.basename.replace(/.bam/, '_per_target_coverage.txt')\n }\n}" }, { "position": 0, "prefix": "--PER_BASE_COVERAGE", "valueFrom": "${\n if(inputs.per_base_coverage){\n return inputs.per_base_coverage\n } else {\n return inputs.input.basename.replace(/.bam/, '_per_base_coverage.txt')\n }\n}" } ], "requirements": [ { "class": "ResourceRequirement", "ramMin": 32000, "coresMin": 1 }, { "class": "DockerRequirement", "dockerPull": "ghcr.io/msk-access/gatk:4.1.8.0" }, { "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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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": "gatk4", "http://usefulinc.com/ns/doap#revision": "4.1.8.0" } ] }, { "class": "CommandLineTool", "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl", "baseCommand": [ "gatk", "CollectInsertSizeMetrics" ], "inputs": [ { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/memory_per_job", "type": [ "null", "int" ], "doc": "Memory per job in megabytes" }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/memory_overhead", "type": [ "null", "int" ], "doc": "Memory overhead per job in megabytes" }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/number_of_threads", "type": [ "null", "int" ] }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/input", "type": "File", "inputBinding": { "position": 0, "prefix": "-I" }, "doc": "Input file (bam or sam). Required." }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/output_file_name", "type": [ "null", "string" ], "doc": "File to write the output to. Required." }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/histogram_file", "type": [ "null", "string" ], "doc": "File to write insert size Histogram chart to. Required." }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/deviations", "type": [ "null", "float" ], "inputBinding": { "position": 0, "prefix": "--DEVIATIONS" }, "doc": "Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and sd grossly misleading regarding the real distribution. Default value: 10.0. This option can be set to 'null' to clear the default value." }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/histogram_width", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--HISTOGRAM_WIDTH" }, "doc": "Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be included. Default value: null." }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/minimum_pct", "type": [ "null", "float" ], "inputBinding": { "position": 0, "prefix": "--MINIMUM_PCT" }, "doc": "When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. This option can be set to 'null' to clear the default value." }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/metrics_acciumulation_level", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--METRIC_ACCUMULATION_LEVEL" }, "doc": "The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list." }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/include_duplicates", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--INCLUDE_DUPLICATES" }, "doc": "If true, also include reads marked as duplicates in the insert size histogram. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/validation_stringency", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--VALIDATION_STRINGENCY" }, "doc": "Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This option can be set to 'null' to clear the default value. Possible values: {STRICT,LENIENT, SILENT}" }, { "default": true, "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/assume_sorted", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--ASSUME_SORTED" }, "doc": "If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}" }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/stop_after", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--STOP_AFTER" }, "doc": "Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value." }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/create_index", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_INDEX" }, "doc": "Whether to create a BAM index when writing a coordinate-sorted BAM file. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/create_md5_file", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_MD5_FILE" }, "doc": "Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/use_jdk_deflater", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--USE_JDK_DEFLATER" }, "doc": "Use the JDK Deflater instead of the Intel Deflater for writing compressed output" }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/use_jdk_inflater", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--USE_JDK_INFLATER" }, "doc": "Use the JDK Inflater instead of the Intel Inflater for reading compressed input" }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/temporary_directory", "type": [ "null", "string" ], "doc": "Default value: null. This option may be specified 0 or more times." } ], "outputs": [ { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/gatk_collect_insert_size_metrics_txt", "type": "File", "outputBinding": { "glob": "${\n if(inputs.output_file_name){\n return inputs.output_file_name\n } else {\n return inputs.input.basename.replace(/.bam/, '_insert_size_metrics.txt')\n }\n}" } }, { "id": "#gatk_collect_insert_size_metrics_4.1.8.0.cwl/gatk_collect_insert_size_metrics_histogram_pdf", "type": "File", "outputBinding": { "glob": "${\n if(inputs.histogram_file){\n return inputs.histogram_file\n } else {\n return inputs.input.basename.replace(/.bam/, '_histogram.pdf')\n }\n}" } } ], "label": "GATK-CollectInsertSizeMetrics", "arguments": [ { "position": 0, "prefix": "--java-options", "valueFrom": "${\n if(inputs.memory_per_job && inputs.memory_overhead) {\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if (inputs.memory_per_job && !inputs.memory_overhead){\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if(!inputs.memory_per_job && inputs.memory_overhead){\n return \"-Xmx15G\"\n }\n else {\n return \"-Xmx15G\"\n }\n}" }, { "position": 0, "prefix": "--TMP_DIR", "valueFrom": "${\n if(inputs.temporary_directory)\n return inputs.temporary_directory;\n return runtime.tmpdir\n}" }, { "position": 2, "prefix": "-O", "valueFrom": "${\n if(inputs.output_file_name){\n return inputs.output_file_name\n } else {\n return inputs.input.basename.replace(/.bam/, '_insert_size_metrics.txt')\n }\n}" }, { "position": 2, "prefix": "-H", "valueFrom": "${\n if(inputs.histogram_file){\n return inputs.histogram_file\n } else {\n return inputs.input.basename.replace(/.bam/, '_histogram.pdf')\n }\n}" } ], "requirements": [ { "class": "ResourceRequirement", "ramMin": 32000, "coresMin": 1 }, { "class": "DockerRequirement", "dockerPull": "ghcr.io/msk-access/gatk:4.1.8.0" }, { "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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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": "gatk4", "http://usefulinc.com/ns/doap#revision": "4.1.8.0" } ] }, { "class": "CommandLineTool", "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl", "baseCommand": [ "gatk", "MeanQualityByCycle" ], "inputs": [ { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/input", "type": "File", "inputBinding": { "position": 0, "prefix": "-I" }, "doc": "An aligned SAM or BAM file. Required." }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/output_file_name", "type": [ "null", "string" ], "doc": "The output file to write the metrics to." }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/chart_output", "type": [ "null", "string" ], "doc": "A file (with .pdf extension) to write the chart to." }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/assume_sorted", "type": [ "null", "boolean" ], "inputBinding": { "position": 1, "prefix": "--ASSUME_SORTED" }, "doc": "If true (default), then the sort order in the header file will be ignored.\n" }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/pf_reads_only", "type": [ "null", "boolean" ], "inputBinding": { "position": 1, "prefix": "--PF_READS_ONLY" }, "doc": "If set to true calculate mean quality over PF reads only. Default value: false. Possible values: {true, false}\n" }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/reference", "type": [ "null", "File" ], "inputBinding": { "position": 0, "prefix": "-R" }, "doc": "Reference sequence file. Note that while this argument is not required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary. Default value: null.", "secondaryFiles": [ "^.fasta.fai", "^.dict" ] }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/validation_stringency", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--VALIDATION_STRINGENCY" }, "doc": "Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This option can be set to 'null' to clear the default value. Possible values: {STRICT,LENIENT, SILENT}" }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/create_index", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_INDEX" }, "doc": "Whether to create a BAM index when writing a coordinate-sorted BAM file. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/create_md5_file", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_MD5_FILE" }, "doc": "Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/memory_per_job", "type": [ "null", "int" ], "doc": "Memory per job in megabytes" }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/memory_overhead", "type": [ "null", "int" ], "doc": "Memory overhead per job in megabytes" }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/number_of_threads", "type": [ "null", "int" ] }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/temporary_directory", "type": [ "null", "string" ], "doc": "Directory with space available to be used by this program for temporary storage of working files." } ], "outputs": [ { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/gatk_mean_quality_by_cycle_output", "type": "File", "outputBinding": { "glob": "${\n if(inputs.output_file_name){\n return inputs.output_file_name\n } else {\n return inputs.input.basename.replace(/.bam/, '_mean_quality_by_cycle.txt')\n }\n}" } }, { "id": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl/gatk_mean_quality_by_cycle_chart_output", "type": "File", "outputBinding": { "glob": "${\n if(inputs.chart_output){\n return inputs.chart_output\n } else {\n return inputs.input.basename.replace(/.bam/, '_mean_quality_by_cycle.pdf')\n }\n}" } } ], "label": "GATK-MeanQualityByCycle", "arguments": [ { "position": 0, "prefix": "--java-options", "valueFrom": "${\n if(inputs.memory_per_job && inputs.memory_overhead) {\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if (inputs.memory_per_job && !inputs.memory_overhead){\n if(inputs.memory_per_job % 1000 == 0) {\n return \"-Xmx\" + (inputs.memory_per_job/1000).toString() + \"G\"\n }\n else {\n return \"-Xmx\" + Math.floor((inputs.memory_per_job/1000)).toString() + \"G\"\n }\n }\n else if(!inputs.memory_per_job && inputs.memory_overhead){\n return \"-Xmx14G\"\n }\n else {\n return \"-Xmx14G\"\n }\n}" }, { "position": 0, "prefix": "--TMP_DIR", "valueFrom": "${\n if(inputs.temporary_directory) {\n return inputs.temporary_directory;\n }\n return runtime.tmpdir;\n}" }, { "position": 0, "prefix": "-O", "valueFrom": "${\n if(inputs.output_file_name){\n return inputs.output_file_name\n } else {\n return inputs.input.basename.replace(/.bam/, '_mean_quality_by_cycle.txt')\n }\n}" }, { "position": 0, "prefix": "--CHART_OUTPUT", "valueFrom": "${\n if(inputs.chart_output){\n return inputs.chart_output\n } else {\n return inputs.input.basename.replace(/.bam/, '_mean_quality_by_cycle.pdf')\n }\n}" } ], "requirements": [ { "class": "ResourceRequirement", "ramMin": 16000, "coresMin": 2 }, { "class": "DockerRequirement", "dockerPull": "ghcr.io/msk-access/gatk:4.1.8.0" }, { "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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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:murphyc4@mskcc.org", "http://xmlns.com/foaf/0.1/name": "Charles 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": "gatk4", "http://usefulinc.com/ns/doap#revision": "4.1.8.0" } ] }, { "class": "CommandLineTool", "id": "#gatk_revert_sam_4.1.8.0.cwl", "baseCommand": [ "gatk", "RevertSam" ], "inputs": [ { "id": "#gatk_revert_sam_4.1.8.0.cwl/input", "type": "File", "inputBinding": { "position": 0, "prefix": "-I" }, "doc": "An aligned SAM or BAM file. Required." }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/output", "type": [ "null", "string" ], "doc": "The output SAM/BAM file to create, or an output directory if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjunction with argument(s) OUTPUT_MAP (OM)" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/output_map", "type": [ "null", "string" ], "doc": "Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjunction with argument(s) OUTPUT (O)" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/attribute_to_clear", "type": [ "null", { "type": "array", "items": "string", "inputBinding": { "position": 0, "prefix": "--ATTRIBUTE_TO_CLEAR" } } ], "doc": "When removing alignment information, the set of optional tags to remove. This may be specified 0 or more times. Default value: [NM, UQ, PG, MD, MQ, SA, MC, AS]." }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/max_discard_fraction", "type": [ "null", "float" ], "inputBinding": { "position": 0, "prefix": "--MAX_DISCARD_FRACTION" }, "doc": "If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to sanitization thenthe program will exit with an Exception instead of exiting cleanly. Output BAM will still be valid. Default value: 0.01." }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/library_name", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--LIBRARY_NAME" }, "doc": "The library name to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same library name. Default value: null." }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/max_records_in_ram", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--MAX_RECORDS_IN_RAM" }, "doc": "When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. Default value: 500000." }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/output_by_readgroup", "type": [ "null", "string" ], "default": "false", "inputBinding": { "position": 0, "prefix": "--OUTPUT_BY_READGROUP" }, "doc": "When true, outputs each read group in a separate file. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/output_by_readgroup_file_format", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--OUTPUT_BY_READGROUP_FILE_FORMAT" }, "doc": "When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format. Default value: dynamic. sam (Generate SAM files.) bam (Generate BAM files.) cram (Generate CRAM files.) dynamic (Generate files based on the extention of INPUT.)" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/remove_alignment_information", "type": [ "null", "string" ], "default": "true", "inputBinding": { "position": 0, "prefix": "--REMOVE_ALIGNMENT_INFORMATION" }, "doc": "Remove all alignment information from the file. Default value: true. Possible values: {true, false}" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/remove_duplicate_information", "type": [ "null", "string" ], "default": "true", "inputBinding": { "position": 1, "prefix": "--REMOVE_DUPLICATE_INFORMATION" }, "doc": "Remove duplicate read flags from all reads. Note that if this is false and\nREMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes\ndesirable trait of having unmapped reads that are marked as duplicates. Default value:\ntrue. Possible values: {true, false}\n" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/restore_hardclips", "type": [ "null", "string" ], "default": "true", "inputBinding": { "position": 0, "prefix": "--RESTORE_HARDCLIPS" }, "doc": "When true, restores reads and qualities of records with hard-clips containing XB and XQ tags. Default value: true. Possible values: {true, false}" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/restore_original_qualities", "type": [ "null", "string" ], "default": "true", "inputBinding": { "position": 1, "prefix": "--RESTORE_ORIGINAL_QUALITIES" }, "doc": "True to restore original qualities from the OQ field to the QUAL field if available. Default value: true. Possible values: {true, false}\n" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/sample_alias", "type": [ "null", "string" ], "inputBinding": { "position": 1, "prefix": "--SAMPLE_ALIAS" }, "doc": "The sample alias to use in the reverted output file. This will override the existing\nsample alias in the file and is used only if all the read groups in the input file have\nthe same sample alias. Default value: null.\n" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/sanitize", "type": [ "null", "string" ], "default": "false", "inputBinding": { "position": 1, "prefix": "--SANITIZE" }, "doc": "WARNING: This option is potentially destructive. If enabled will discard reads in order to\nproduce a consistent output BAM. Reads discarded include (but are not limited to) paired\nreads with missing mates, duplicated records, records with mismatches in length of bases\nand qualities. This option can only be enabled if the output sort order is queryname and\nwill always cause sorting to occur. Default value: false. Possible values: {true, false}\n" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/sort_order", "type": [ "null", "string" ], "inputBinding": { "position": 1, "prefix": "--SORT_ORDER" }, "doc": "The sort order to create the reverted output file with. Default value: queryname. Possible values: {unsorted, queryname, coordinate, duplicate, unknown}\n" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/reference", "type": [ "null", "File" ], "inputBinding": { "position": 0, "prefix": "-R" }, "doc": "Reference sequence file. Note that while this argument is not required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary. Default value: null.", "secondaryFiles": [ "^.fasta.fai", "^.dict" ] }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/validation_stringency", "type": [ "null", "string" ], "inputBinding": { "position": 0, "prefix": "--VALIDATION_STRINGENCY" }, "doc": "Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This option can be set to 'null' to clear the default value. Possible values: {STRICT,LENIENT, SILENT}" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/compression_level", "type": [ "null", "int" ], "inputBinding": { "position": 0, "prefix": "--COMPRESSION_LEVEL" }, "doc": "Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2." }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/create_index", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_INDEX" }, "doc": "Whether to create a BAM index when writing a coordinate-sorted BAM file. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/create_md5_file", "type": [ "null", "boolean" ], "inputBinding": { "position": 0, "prefix": "--CREATE_MD5_FILE" }, "doc": "Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: false. Possible values: {true, false}" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/memory_per_job", "type": [ "null", "int" ], "doc": "Memory per job in megabytes" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/memory_overhead", "type": [ "null", "int" ], "doc": "Memory overhead per job in megabytes" }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/number_of_threads", "type": [ "null", "int" ] }, { "id": "#gatk_revert_sam_4.1.8.0.cwl/temporary_directory", "type": [ "null", "string" ], "doc": "Default value: null. 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"#qc_uncollapsed_bam.cwl/bam_qc_stats_pool_b/gatk_collect_insert_size_metrics_histogram_pdf" }, { "id": "#qc_uncollapsed_bam.cwl/bam_qc_stats_pool_b/gatk_collect_insert_size_metrics_txt" }, { "id": "#qc_uncollapsed_bam.cwl/bam_qc_stats_pool_b/gatk_collect_hs_metrics_txt" }, { "id": "#qc_uncollapsed_bam.cwl/bam_qc_stats_pool_b/gatk_collect_hs_metrics_per_base_coverage_txt" }, { "id": "#qc_uncollapsed_bam.cwl/bam_qc_stats_pool_b/gatk_collect_hs_metrics_per_target_coverage_txt" }, { "id": "#qc_uncollapsed_bam.cwl/bam_qc_stats_pool_b/gatk_collect_alignment_summary_metrics_txt" } ], "run": "#bam_qc_stats.cwl", "label": "bam_qc_stats_pool_b", "https://www.sevenbridges.com/x": 738.7452392578125, "https://www.sevenbridges.com/y": 599.34375 }, { "id": "#qc_uncollapsed_bam.cwl/gatk_mean_quality_by_cycle_4_1_8_1", "in": [ { "id": "#qc_uncollapsed_bam.cwl/gatk_mean_quality_by_cycle_4_1_8_1/input", "source": "#qc_uncollapsed_bam.cwl/uncollapsed_bam_base_recal" }, { "id": "#qc_uncollapsed_bam.cwl/gatk_mean_quality_by_cycle_4_1_8_1/reference", "source": "#qc_uncollapsed_bam.cwl/reference" } ], "out": [ { "id": "#qc_uncollapsed_bam.cwl/gatk_mean_quality_by_cycle_4_1_8_1/gatk_mean_quality_by_cycle_output" }, { "id": "#qc_uncollapsed_bam.cwl/gatk_mean_quality_by_cycle_4_1_8_1/gatk_mean_quality_by_cycle_chart_output" } ], "run": "#gatk_mean_quality_by_cycle_4.1.8.0.cwl", "label": "GATK-MeanQualityByCycle_base_recal", "https://www.sevenbridges.com/x": 351.4375, "https://www.sevenbridges.com/y": 701.7890625 }, { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0", "in": [ { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0/input", "source": "#qc_uncollapsed_bam.cwl/uncollapsed_bam_base_recal" }, { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0/remove_alignment_information", "default": "false" }, { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0/remove_duplicate_information", "default": "true" }, { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0/restore_hardclips", "default": "false" }, { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0/restore_original_qualities", "default": "false" }, { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0/sort_order", "default": "unsorted" }, { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0/validation_stringency", "default": "SILENT" } ], "out": [ { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0/gatk_revert_sam_output" }, { "id": "#qc_uncollapsed_bam.cwl/gatk_revert_sam_4_1_8_0/gatk_revert_sam_output_map" } ], "run": "#gatk_revert_sam_4.1.8.0.cwl", "label": "GATK-RevertSam", "https://www.sevenbridges.com/x": 351.4375, "https://www.sevenbridges.com/y": 580.8984375 } ], "requirements": [ { "class": "SubworkflowFeatureRequirement" } ] }, { "class": "Workflow", "id": "#qc_aggregator.cwl", "label": "qc_aggregator", "inputs": [ { "id": "#qc_aggregator.cwl/duplex_extraction_files", "type": { "type": "array", "items": "File" }, "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.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 533.546875 }, { "id": "#qc_aggregator.cwl/duplex_biometrics_discordance_threshold", "type": [ "null", "float" ], "doc": "Discordance values less than this are regarded as matching samples. (default: 0.05)", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 853.6875 }, { "id": "#qc_aggregator.cwl/biometrics_json", "type": [ "null", "boolean" ], "label": "biometrics_json", "doc": "Also output data in JSON format.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 2454.3125 }, { "id": "#qc_aggregator.cwl/biometrics_plot", "type": [ "null", "boolean" ], "label": "biometrics_plot", "doc": "Also output plots of the data.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 2347.59375 }, { "id": "#qc_aggregator.cwl/simplex_bam_pool_a_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "simplex_bam_pool_a_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 320.109375 }, { "id": "#qc_aggregator.cwl/simplex_bam_pool_b_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "simplex_bam_pool_b_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 213.40625 }, { "id": "#qc_aggregator.cwl/duplex_bam_sequence_qc_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "duplex_bam_sequence_qc_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 1173.796875 }, { "id": "#qc_aggregator.cwl/duplex_bam_stats_pool_a_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "duplex_bam_stats_pool_a_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 1067.09375 }, { "id": "#qc_aggregator.cwl/duplex_bam_stats_pool_b_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "duplex_bam_stats_pool_b_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 960.390625 }, { "id": "#qc_aggregator.cwl/collapsed_bam_stats_pool_a_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "collapsed_bam_stats_pool_a_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 1920.78125 }, { "id": "#qc_aggregator.cwl/collapsed_bam_stats_pool_b_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "collapsed_bam_stats_pool_b_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 1814.078125 }, { "id": "#qc_aggregator.cwl/collapsed_bam_duplex_metrics_pool_a_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "collapsed_bam_duplex_metrics_pool_a_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 2134.1875 }, { "id": "#qc_aggregator.cwl/collapsed_bam_duplex_metrics_pool_b_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "collapsed_bam_duplex_metrics_pool_b_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 2027.484375 }, { "id": "#qc_aggregator.cwl/gatk_mean_quality_by_cycle_recal_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "gatk_mean_quality_by_cycle_recal_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 426.828125 }, { "id": "#qc_aggregator.cwl/uncollapsed_bam_stats_pool_b_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "uncollapsed_bam_stats_pool_b_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 0 }, { "id": "#qc_aggregator.cwl/uncollapsed_bam_stats_pool_a_dir", "type": { "type": "array", "items": [ "File", "Directory", "null" ] }, "label": "uncollapsed_bam_stats_pool_a_dir", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 106.703125 }, { "id": "#qc_aggregator.cwl/biometrics_threads", "type": [ "null", "int" ], "label": "biometrics_threads", "doc": "Number of threads to use.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 2240.890625 }, { "id": "#qc_aggregator.cwl/duplex_biometrics_major_threshold", "type": [ "null", "float" ], "label": "duplex_biometrics_major_threshold", "doc": "Major contamination threshold for bad sample.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 746.96875 }, { "id": "#qc_aggregator.cwl/duplex_biometrics_minor_threshold", "type": [ "null", "float" ], "label": "duplex_biometrics_minor_threshold", "doc": "Minor contamination threshold for bad sample.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 640.25 }, { "id": "#qc_aggregator.cwl/collapsed_extraction_files", "type": { "type": "array", "items": "File" }, "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.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 1280.5 }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_discordance_threshold", "type": [ "null", "float" ], "label": "collapsed_biometrics_discordance_threshold", "doc": "Discordance values less than this are regarded as matching samples. (default: 0.05)", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 1600.640625 }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_major_threshold", "type": [ "null", "float" ], "label": "collapsed_biometrics_major_threshold", "doc": "Major contamination threshold for bad sample.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 1493.921875 }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor_threshold", "type": [ "null", "float" ], "label": "collapsed_biometrics_minor_threshold", "doc": "Minor contamination threshold for bad sample.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 1387.203125 }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_coverage_threshold", "type": [ "null", "int" ], "label": "collapsed_biometrics_coverage_threshold", "doc": "Samples with Y chromosome above this value will be considered male.", "https://www.sevenbridges.com/x": 0, "https://www.sevenbridges.com/y": 1707.359375 } ], "outputs": [ { "id": "#qc_aggregator.cwl/aggregate_qc_stats", "outputSource": [ "#qc_aggregator.cwl/final_aggregate/directory" ], "type": "Directory", "label": "aggregate_qc_stats", "https://www.sevenbridges.com/x": 1217.726806640625, "https://www.sevenbridges.com/y": 1330.7305908203125 } ], "steps": [ { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype", "in": [ { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/input", "source": [ "#qc_aggregator.cwl/duplex_extraction_files" ] }, { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/discordance_threshold", "source": "#qc_aggregator.cwl/duplex_biometrics_discordance_threshold" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/prefix", "default": "duplex" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/plot", "default": true, "source": "#qc_aggregator.cwl/biometrics_plot" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/json", "default": true, "source": "#qc_aggregator.cwl/biometrics_json" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/threads", "source": "#qc_aggregator.cwl/biometrics_threads" } ], "out": [ { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_comparisons" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_cluster_input" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_cluster_input_database" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_plot_input" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_plot_input_database" } ], "run": "#biometrics_genotype.cwl", "https://www.sevenbridges.com/x": 410.1875, "https://www.sevenbridges.com/y": 1004.078125 }, { "id": "#qc_aggregator.cwl/aggregate", "in": [ { "id": "#qc_aggregator.cwl/aggregate/files", "source": [ "#qc_aggregator.cwl/simplex_bam_pool_a_dir", "#qc_aggregator.cwl/simplex_bam_pool_b_dir", "#qc_aggregator.cwl/duplex_bam_stats_pool_a_dir", "#qc_aggregator.cwl/duplex_bam_stats_pool_b_dir", "#qc_aggregator.cwl/collapsed_bam_stats_pool_a_dir", "#qc_aggregator.cwl/collapsed_bam_stats_pool_b_dir", "#qc_aggregator.cwl/collapsed_bam_duplex_metrics_pool_a_dir", "#qc_aggregator.cwl/collapsed_bam_duplex_metrics_pool_b_dir", "#qc_aggregator.cwl/gatk_mean_quality_by_cycle_recal_dir", "#qc_aggregator.cwl/uncollapsed_bam_stats_pool_b_dir", "#qc_aggregator.cwl/uncollapsed_bam_stats_pool_a_dir", "#qc_aggregator.cwl/duplex_bam_sequence_qc_dir" ] }, { "id": "#qc_aggregator.cwl/aggregate/output_directory_name", "default": [ "simplex_bam_pool_a_dir", "simplex_bam_pool_b_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", "uncollapsed_bam_stats_pool_b_dir", "uncollapsed_bam_stats_pool_a_dir", "duplex_bam_sequence_qc_dir" ] } ], "out": [ { "id": "#qc_aggregator.cwl/aggregate/directory" } ], "run": "#put_in_dir.cwl", "label": "aggregate", "scatter": [ "#qc_aggregator.cwl/aggregate/files", "#qc_aggregator.cwl/aggregate/output_directory_name" ], "scatterMethod": "dotproduct", "https://www.sevenbridges.com/x": 410.1875, "https://www.sevenbridges.com/y": 1733.6875 }, { "id": "#qc_aggregator.cwl/duplex_biometrics_major", "in": [ { "id": "#qc_aggregator.cwl/duplex_biometrics_major/input", "source": [ "#qc_aggregator.cwl/duplex_extraction_files" ] }, { "id": "#qc_aggregator.cwl/duplex_biometrics_major/major_threshold", "source": "#qc_aggregator.cwl/duplex_biometrics_major_threshold" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_major/prefix", "default": "duplex" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_major/plot", "default": true, "source": "#qc_aggregator.cwl/biometrics_plot" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_major/json", "default": true, "source": "#qc_aggregator.cwl/biometrics_json" } ], "out": [ { "id": "#qc_aggregator.cwl/duplex_biometrics_major/biometrics_major_csv" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_major/biometrics_major_json" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_major/biometrics_major_plot" } ], "run": "#biometrics_major.cwl", "label": "duplex_biometrics_major", "https://www.sevenbridges.com/x": 410.1875, "https://www.sevenbridges.com/y": 848.34375 }, { "id": "#qc_aggregator.cwl/duplex_biometrics_minor", "in": [ { "id": "#qc_aggregator.cwl/duplex_biometrics_minor/input", "source": [ "#qc_aggregator.cwl/duplex_extraction_files" ] }, { "id": "#qc_aggregator.cwl/duplex_biometrics_minor/minor_threshold", "source": "#qc_aggregator.cwl/duplex_biometrics_minor_threshold" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_minor/prefix", "default": "duplex" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_minor/plot", "default": true, "source": "#qc_aggregator.cwl/biometrics_plot" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_minor/json", "default": true, "source": "#qc_aggregator.cwl/biometrics_json" } ], "out": [ { "id": "#qc_aggregator.cwl/duplex_biometrics_minor/biometrics_minor_csv" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_minor/biometrics_minor_json" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_minor/biometrics_minor_plot" }, { "id": "#qc_aggregator.cwl/duplex_biometrics_minor/biometrics_minor_sites_plot" } ], "run": "#biometrics_minor.cwl", "label": "duplex_biometrics_minor", "https://www.sevenbridges.com/x": 410.1875, "https://www.sevenbridges.com/y": 699.625 }, { "id": "#qc_aggregator.cwl/duplex_biometrics_agg", "in": [ { "id": "#qc_aggregator.cwl/duplex_biometrics_agg/files", "source": [ "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_plot_input_database", "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_plot_input", "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_comparisons", "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_cluster_input_database", "#qc_aggregator.cwl/duplex_biometrics_genotype/biometrics_genotype_cluster_input", "#qc_aggregator.cwl/duplex_biometrics_major/biometrics_major_plot", "#qc_aggregator.cwl/duplex_biometrics_major/biometrics_major_json", "#qc_aggregator.cwl/duplex_biometrics_major/biometrics_major_csv", "#qc_aggregator.cwl/duplex_biometrics_minor/biometrics_minor_sites_plot", "#qc_aggregator.cwl/duplex_biometrics_minor/biometrics_minor_plot", "#qc_aggregator.cwl/duplex_biometrics_minor/biometrics_minor_json", "#qc_aggregator.cwl/duplex_biometrics_minor/biometrics_minor_csv" ] }, { "id": "#qc_aggregator.cwl/duplex_biometrics_agg/output_directory_name", "default": "duplex_biometrics_output" } ], "out": [ { "id": "#qc_aggregator.cwl/duplex_biometrics_agg/directory" } ], "run": "#put_in_dir.cwl", "label": "duplex_biometrics_agg", "https://www.sevenbridges.com/x": 750.1968994140625, "https://www.sevenbridges.com/y": 1131.8909912109375 }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype", "in": [ { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/input", "source": [ "#qc_aggregator.cwl/collapsed_extraction_files" ] }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/discordance_threshold", "source": "#qc_aggregator.cwl/collapsed_biometrics_discordance_threshold" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/prefix", "default": "collapsed" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/plot", "default": true, "source": "#qc_aggregator.cwl/biometrics_plot" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/json", "default": true, "source": "#qc_aggregator.cwl/biometrics_json" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/threads", "source": "#qc_aggregator.cwl/biometrics_threads" } ], "out": [ { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_comparisons" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_cluster_input" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_cluster_input_database" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_plot_input" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_plot_input_database" } ], "run": "#biometrics_genotype.cwl", "label": "collapsed_biometrics_genotype", "https://www.sevenbridges.com/x": 410.1875, "https://www.sevenbridges.com/y": 1598.953125 }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_major", "in": [ { "id": "#qc_aggregator.cwl/collapsed_biometrics_major/input", "source": [ "#qc_aggregator.cwl/collapsed_extraction_files" ] }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_major/major_threshold", "default": 0.6, "source": "#qc_aggregator.cwl/collapsed_biometrics_major_threshold" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_major/prefix", "default": "collapsed" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_major/plot", "default": true, "source": "#qc_aggregator.cwl/biometrics_plot" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_major/json", "default": true, "source": "#qc_aggregator.cwl/biometrics_json" } ], "out": [ { "id": "#qc_aggregator.cwl/collapsed_biometrics_major/biometrics_major_csv" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_major/biometrics_major_json" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_major/biometrics_major_plot" } ], "run": "#biometrics_major.cwl", "label": "collapsed_biometrics_major", "https://www.sevenbridges.com/x": 410.1875, "https://www.sevenbridges.com/y": 1443.21875 }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor", "in": [ { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/input", "source": [ "#qc_aggregator.cwl/collapsed_extraction_files" ] }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/minor_threshold", "default": 0.002, "source": "#qc_aggregator.cwl/collapsed_biometrics_minor_threshold" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/prefix", "default": "collapsed" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/plot", "default": true, "source": "#qc_aggregator.cwl/biometrics_plot" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/json", "default": true, "source": "#qc_aggregator.cwl/biometrics_json" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/no_db_comparison", "default": false } ], "out": [ { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/biometrics_minor_csv" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/biometrics_minor_json" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/biometrics_minor_plot" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_minor/biometrics_minor_sites_plot" } ], "run": "#biometrics_minor.cwl", "label": "collapsed_biometrics_minor", "https://www.sevenbridges.com/x": 410.1875, "https://www.sevenbridges.com/y": 1294.5 }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_sexmismatch", "in": [ { "id": "#qc_aggregator.cwl/collapsed_biometrics_sexmismatch/input", "source": [ "#qc_aggregator.cwl/collapsed_extraction_files" ] }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_sexmismatch/coverage_threshold", "source": "#qc_aggregator.cwl/collapsed_biometrics_coverage_threshold" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_sexmismatch/prefix", "default": "collapsed" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_sexmismatch/json", "default": true, "source": "#qc_aggregator.cwl/biometrics_json" } ], "out": [ { "id": "#qc_aggregator.cwl/collapsed_biometrics_sexmismatch/biometrics_sexmismatch_csv" }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_sexmismatch/biometrics_sexmismatch_json" } ], "run": "#biometrics_sexmismatch.cwl", "label": "collapsed_biometrics_sexmismatch", "https://www.sevenbridges.com/x": 410.1875, "https://www.sevenbridges.com/y": 1152.796875 }, { "id": "#qc_aggregator.cwl/collapsed_biometrics_agg", "in": [ { "id": "#qc_aggregator.cwl/collapsed_biometrics_agg/files", "source": [ "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_plot_input_database", "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_plot_input", "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_comparisons", "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_cluster_input_database", "#qc_aggregator.cwl/collapsed_biometrics_genotype/biometrics_genotype_cluster_input", "#qc_aggregator.cwl/collapsed_biometrics_major/biometrics_major_plot", "#qc_aggregator.cwl/collapsed_biometrics_major/biometrics_major_json", "#qc_aggregator.cwl/collapsed_biometrics_major/biometrics_major_csv", "#qc_aggregator.cwl/collapsed_biometrics_minor/biometrics_minor_sites_plot", "#qc_aggregator.cwl/collapsed_biometrics_minor/biometrics_minor_plot", "#qc_aggregator.cwl/collapsed_biometrics_minor/biometrics_minor_json", 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"all_qc_files" } ], "out": [ { "id": "#qc_aggregator.cwl/final_aggregate/directory" } ], "run": "#put_in_dir.cwl", "label": "final_aggregate", "https://www.sevenbridges.com/x": 1054.649169921875, "https://www.sevenbridges.com/y": 1227.1484375 } ], "requirements": [ { "class": "ScatterFeatureRequirement" }, { "class": "MultipleInputFeatureRequirement" } ] }, { "class": "Workflow", "id": "#qc_generator.cwl", "label": "qc_generator", "inputs": [ { "id": "#qc_generator.cwl/reference", "type": "File", "secondaryFiles": [ "^.fasta.fai", "^.dict" ] }, { "id": "#qc_generator.cwl/duplex_bam", "type": "File", "label": "duplex_bam", "secondaryFiles": [ "^.bai" ] }, { "id": "#qc_generator.cwl/collapsed_bam", "type": "File", "label": "collapsed_bam", "secondaryFiles": [ "^.bai" ] }, { "id": "#qc_generator.cwl/group_reads_by_umi_bam", "type": "File", "label": "group_reads_by_umi_bam", "doc": "Input BAM file generated by GroupReadByUmi." }, { "id": "#qc_generator.cwl/uncollapsed_bam_base_recal", "type": "File", "label": "uncollapsed_bam_base_recal", "doc": "An aligned SAM or BAM file. Required.", "secondaryFiles": [ "^.bai" ] }, { "id": "#qc_generator.cwl/pool_b_target_intervals", "type": "File", "label": "pool_b_target_intervals" }, { "id": "#qc_generator.cwl/pool_b_bait_intervals", "type": "File", "label": "pool_b_bait_intervals" }, { "id": "#qc_generator.cwl/pool_a_target_intervals", "type": "File", "label": "pool_a_target_intervals" }, { "id": "#qc_generator.cwl/pool_a_bait_intervals", "type": "File", "label": "pool_a_bait_intervals" }, { "id": "#qc_generator.cwl/noise_sites_bed", "type": "File", "label": "noise_sites_bed", "doc": "Path to BED file containing regions over which to calculate noise [required]" }, { "id": "#qc_generator.cwl/sample_sex", "type": [ "null", "string" ], "doc": "Expected sample sex (i.e. M or F)." }, { "id": "#qc_generator.cwl/sample_name", "type": [ "null", "string" ], "doc": "Sample name. If not specified, sample name is automatically figured out from the BAM file." }, { "id": "#qc_generator.cwl/sample_group", "type": "string", "doc": "The sample group (e.g. the sample patient ID)." }, { "id": "#qc_generator.cwl/simplex_bam", "type": "File", "label": "simplex_bam", "secondaryFiles": [ "^.bai" ] }, { "id": "#qc_generator.cwl/biometrics_plot", "type": [ "null", "boolean" ], "label": "biometrics_plot", "doc": "Also output plots of the data." }, { "id": "#qc_generator.cwl/duplex_biometrics_major_threshold", "type": [ "null", "float" ], "label": "duplex_biometrics_major_threshold", "doc": "Major contamination threshold for bad sample." }, { "id": "#qc_generator.cwl/biometrics_json", "type": [ "null", "boolean" ], "label": "biometrics_json", "doc": "Also output data in JSON format." }, { "id": "#qc_generator.cwl/collapsed_biometrics_minor_threshold", "type": [ "null", "float" ], "label": "collapsed_biometrics_minor_threshold", "doc": "Minor contamination threshold for bad sample." }, { "id": "#qc_generator.cwl/collapsed_biometrics_coverage_threshold", "type": [ "null", "int" ], "label": "collapsed_biometrics_coverage_threshold", "doc": "Samples with Y chromosome above this value will be considered male." }, { "id": "#qc_generator.cwl/sequence_qc_min_basq", "type": [ "null", "int" ] }, { "id": "#qc_generator.cwl/sequence_qc_min_mapq", "type": [ "null", "int" ] }, { "id": "#qc_generator.cwl/sequence_qc_threshold", "type": [ "null", "float" ] }, { "id": "#qc_generator.cwl/sequence_qc_truncate", "type": [ "null", "int" ] }, { "id": "#qc_generator.cwl/hsmetrics_minimum_mapping_quality", "type": [ "null", "int" ] }, { "id": "#qc_generator.cwl/hsmetrics_minimum_base_quality", "type": [ "null", "int" ] }, { "id": "#qc_generator.cwl/hsmetrics_coverage_cap", "type": [ "null", "int" ] }, { "id": "#qc_generator.cwl/vcf_file", "type": "File" }, { "id": "#qc_generator.cwl/hotspots_maf", "type": "File" } ], "outputs": [ { "id": "#qc_generator.cwl/uncollapsed_bam_stats_pool_a_dir", "outputSource": [ "#qc_generator.cwl/uncollapsed_bam_stats_pool_a/directory" ], "type": "Directory", "label": "uncollapsed_bam_stats_pool_a_dir" }, { "id": "#qc_generator.cwl/uncollapsed_bam_stats_pool_b_dir", "outputSource": [ "#qc_generator.cwl/uncollapsed_bam_stats_pool_b/directory" ], "type": "Directory", "label": "uncollapsed_bam_stats_pool_b_dir" }, { "id": "#qc_generator.cwl/gatk_mean_quality_by_cycle_recal_dir", "outputSource": [ "#qc_generator.cwl/gatk_mean_quality_by_cycle_recal/directory" ], "type": "Directory", "label": "gatk_mean_quality_by_cycle_recal_dir" }, { "id": "#qc_generator.cwl/collapsed_bam_biometrics_dir", "outputSource": [ "#qc_generator.cwl/collapsed_bam_biometrics/directory" ], "type": "Directory", "label": "collapsed_bam_biometrics_dir" }, { "id": "#qc_generator.cwl/collapsed_bam_duplex_metrics_pool_b_dir", "outputSource": [ "#qc_generator.cwl/collapsed_bam_duplex_metrics_pool_b/directory" ], "type": 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"#qc_generator.cwl/simplex_bam_pool_b/directory" ], "type": "Directory", "label": "simplex_bam_pool_b_dir" }, { "id": "#qc_generator.cwl/duplex_bam_sequence_qc_dir", "outputSource": [ "#qc_generator.cwl/duplex_bam_sequence_qc/directory" ], "type": "Directory", "label": "duplex_bam_sequence_qc_dir" }, { "id": "#qc_generator.cwl/duplex_bam_stats_pool_a_dir", "outputSource": [ "#qc_generator.cwl/duplex_bam_stats_pool_a/directory" ], "type": "Directory", "label": "duplex_bam_stats_pool_a_dir" }, { "id": "#qc_generator.cwl/duplex_bam_stats_pool_b_dir", "outputSource": [ "#qc_generator.cwl/duplex_bam_stats_pool_b/directory" ], "type": "Directory", "label": "duplex_bam_stats_pool_b_dir" }, { "id": "#qc_generator.cwl/duplex_bam_biometrics_dir", "outputSource": [ "#qc_generator.cwl/duplex_bam_biometrics/directory" ], "type": "Directory", "label": "duplex_bam_biometrics_dir" }, { "id": "#qc_generator.cwl/duplex_bam_genotyping_maf", "outputSource": [ "#qc_generator.cwl/qc_duplex_bam/fillout_maf" ], "type": "File", "label": "duplex_bam_genotyping_maf" }, { "id": "#qc_generator.cwl/duplex_biometrics_extract_pickle", "outputSource": [ "#qc_generator.cwl/qc_duplex_bam/biometrics_extract_pickle" ], "type": "File" }, { "id": "#qc_generator.cwl/collapsed_biometrics_extract_pickle", "outputSource": [ "#qc_generator.cwl/qc_collapsed_bam/biometrics_extract_pickle" ], "type": "File" }, { "id": "#qc_generator.cwl/collapsed_bam_genotyping_maf", "outputSource": [ "#qc_generator.cwl/qc_collapsed_bam/fillout_maf" ], "type": "File" } ], "steps": [ { "id": "#qc_generator.cwl/qc_collapsed_bam", "in": [ { "id": "#qc_generator.cwl/qc_collapsed_bam/reference", "source": "#qc_generator.cwl/reference" }, { "id": "#qc_generator.cwl/qc_collapsed_bam/pool_b_target_intervals", "source": "#qc_generator.cwl/pool_b_target_intervals" }, { "id": "#qc_generator.cwl/qc_collapsed_bam/pool_a_target_intervals", "source": "#qc_generator.cwl/pool_a_target_intervals" }, { "id": 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