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| "id": "#exomeseq-gatk4-01-preprocessing.cwl/recalibrate_02_apply_bqsr/output_recalibrated_bam_filename" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/reference_genome", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/recalibrate_02_apply_bqsr/reference" | |
| } | |
| ], | |
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| "#exomeseq-gatk4-01-preprocessing.cwl/recalibrate_02_apply_bqsr/output_recalibrated_bam" | |
| ], | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/recalibrate_02_apply_bqsr" | |
| }, | |
| { | |
| "run": "#GATK4-SortSam.cwl", | |
| "requirements": [ | |
| { | |
| "class": "ResourceRequirement", | |
| "ramMin": 5000 | |
| } | |
| ], | |
| "in": [ | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/map/output", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/sort/input_file" | |
| }, | |
| { | |
| "default": "-Xms4000m", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/sort/java_opt" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/generate_sample_filenames/sorted_reads_output_filename", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/sort/output_sorted_bam_filename" | |
| }, | |
| { | |
| "default": "coordinate", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/sort/sort_order" | |
| } | |
| ], | |
| "out": [ | |
| "#exomeseq-gatk4-01-preprocessing.cwl/sort/output_sorted_bam" | |
| ], | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/sort" | |
| }, | |
| { | |
| "run": "#trim_galore.cwl", | |
| "requirements": [ | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 4, | |
| "ramMin": 8000 | |
| } | |
| ], | |
| "in": [ | |
| { | |
| "default": true, | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/trim/paired" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/combine_reads/output", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/trim/reads" | |
| } | |
| ], | |
| "out": [ | |
| "#exomeseq-gatk4-01-preprocessing.cwl/trim/trimmed_reads", | |
| "#exomeseq-gatk4-01-preprocessing.cwl/trim/trim_reports" | |
| ], | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/trim" | |
| }, | |
| { | |
| "run": "#GATK4-HaplotypeCaller.cwl", | |
| "requirements": [ | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "ramMin": 8192 | |
| } | |
| ], | |
| "in": [ | |
| { | |
| "default": [ | |
| "StandardAnnotation", | |
| "AS_StandardAnnotation" | |
| ], | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/annotation_groups" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/resource_dbsnp", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/dbnsp" | |
| }, | |
| { | |
| "default": "GVCF", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/emit_ref_confidence" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/recalibrate_02_apply_bqsr/output_recalibrated_bam", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/input_bam" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/interval_padding", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/interval_padding" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/intervals", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/intervals" | |
| }, | |
| { | |
| "default": "-Xms7000m", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/java_opt" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/generate_sample_filenames/haplotypes_bam_output_filename", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/output_bam_filename" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/generate_sample_filenames/raw_variants_output_filename", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/output_variants_filename" | |
| }, | |
| { | |
| "source": "#exomeseq-gatk4-01-preprocessing.cwl/reference_genome", | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/reference" | |
| } | |
| ], | |
| "out": [ | |
| "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/output_variants", | |
| "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling/output_bam" | |
| ], | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl/variant_calling" | |
| } | |
| ], | |
| "id": "#exomeseq-gatk4-01-preprocessing.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "broadinstitute/gatk:4.0.4.0" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "hints": [ | |
| { | |
| "class": "SoftwareRequirement", | |
| "packages": [ | |
| { | |
| "version": [ | |
| "4.0.4.0" | |
| ], | |
| "https://schema.org/citation": "https://doi.org/10.1101/gr.107524.110", | |
| "package": "gatk" | |
| } | |
| ] | |
| } | |
| ], | |
| "baseCommand": "gatk", | |
| "inputs": [ | |
| { | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "--add-output-sam-program-record" | |
| }, | |
| "id": "#GATK4-ApplyBQSR.cwl/add_output_sam_program_record" | |
| }, | |
| { | |
| "type": "File", | |
| "doc": "BQSR recalibration report", | |
| "inputBinding": { | |
| "prefix": "-bqsr" | |
| }, | |
| "id": "#GATK4-ApplyBQSR.cwl/bqsr_report" | |
| }, | |
| { | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "-I" | |
| }, | |
| "secondaryFiles": [ | |
| "^.bai" | |
| ], | |
| "doc": "input bam", | |
| "id": "#GATK4-ApplyBQSR.cwl/input_bam" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "int" | |
| ], | |
| "doc": "Amount of padding (in bp) to add to each interval you are including. Defaults to 0", | |
| "inputBinding": { | |
| "prefix": "-ip" | |
| }, | |
| "id": "#GATK4-ApplyBQSR.cwl/interval_padding" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| { | |
| "type": "array", | |
| "items": "File", | |
| "inputBinding": { | |
| "prefix": "-L" | |
| } | |
| } | |
| ], | |
| "doc": "One or more genomic intervals over which to operate", | |
| "id": "#GATK4-ApplyBQSR.cwl/intervals" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "String of options to pass to JVM at runtime", | |
| "inputBinding": { | |
| "prefix": "--java-options", | |
| "position": -1, | |
| "shellQuote": true | |
| }, | |
| "id": "#GATK4-ApplyBQSR.cwl/java_opt" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Output BAM filename", | |
| "default": "recalibrated.bam", | |
| "inputBinding": { | |
| "prefix": "-O" | |
| }, | |
| "id": "#GATK4-ApplyBQSR.cwl/output_recalibrated_bam_filename" | |
| }, | |
| { | |
| "type": "File", | |
| "inputBinding": { | |
| "position": 2, | |
| "prefix": "-R" | |
| }, | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".pac", | |
| ".sa", | |
| ".fai", | |
| "^.dict" | |
| ], | |
| "id": "#GATK4-ApplyBQSR.cwl/reference" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| { | |
| "type": "array", | |
| "items": "int", | |
| "inputBinding": { | |
| "prefix": "--static-quantized-quals" | |
| } | |
| } | |
| ], | |
| "doc": "Use static quantized quality scores to a given number of levels (with -bqsr)", | |
| "id": "#GATK4-ApplyBQSR.cwl/static_quantized_quals" | |
| }, | |
| { | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "--use-original-qualities" | |
| }, | |
| "id": "#GATK4-ApplyBQSR.cwl/use_original_qualities" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.output_recalibrated_bam_filename)" | |
| }, | |
| "secondaryFiles": [ | |
| "^.bai" | |
| ], | |
| "id": "#GATK4-ApplyBQSR.cwl/output_recalibrated_bam" | |
| } | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "ApplyBQSR", | |
| "position": 0 | |
| } | |
| ], | |
| "id": "#GATK4-ApplyBQSR.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "broadinstitute/gatk:4.0.4.0" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "hints": [ | |
| { | |
| "class": "SoftwareRequirement", | |
| "packages": [ | |
| { | |
| "version": [ | |
| "4.0.4.0" | |
| ], | |
| "https://schema.org/citation": "https://doi.org/10.1101/gr.107524.110", | |
| "package": "gatk" | |
| } | |
| ] | |
| } | |
| ], | |
| "baseCommand": "gatk", | |
| "inputs": [ | |
| { | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "-I" | |
| }, | |
| "secondaryFiles": [ | |
| "^.bai" | |
| ], | |
| "doc": "input bam", | |
| "id": "#GATK4-BaseRecalibrator.cwl/input_bam" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "int" | |
| ], | |
| "doc": "Amount of padding (in bp) to add to each interval you are including. Defaults to 0", | |
| "inputBinding": { | |
| "prefix": "-ip" | |
| }, | |
| "id": "#GATK4-BaseRecalibrator.cwl/interval_padding" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| { | |
| "type": "array", | |
| "items": "File", | |
| "inputBinding": { | |
| "prefix": "-L" | |
| } | |
| } | |
| ], | |
| "doc": "One or more genomic intervals over which to operate", | |
| "id": "#GATK4-BaseRecalibrator.cwl/intervals" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "String of options to pass to JVM at runtime", | |
| "inputBinding": { | |
| "prefix": "--java-options", | |
| "position": -1, | |
| "shellQuote": true | |
| }, | |
| "id": "#GATK4-BaseRecalibrator.cwl/java_opt" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| { | |
| "type": "array", | |
| "items": "File", | |
| "inputBinding": { | |
| "prefix": "--known-sites" | |
| } | |
| } | |
| ], | |
| "secondaryFiles": [ | |
| ".idx" | |
| ], | |
| "doc": "Any number of VCF files representing known SNPs and/or indels. Could be e.g. dbSNP and/or official 1000 Genomes indel calls. SNPs in these files will be ignored unless the --mismatchFraction argument is used. optional parameter.", | |
| "id": "#GATK4-BaseRecalibrator.cwl/known_sites" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Recalibration Report Filename", | |
| "default": "recal.csv", | |
| "inputBinding": { | |
| "prefix": "-O" | |
| }, | |
| "id": "#GATK4-BaseRecalibrator.cwl/output_recalibration_report_filename" | |
| }, | |
| { | |
| "type": "File", | |
| "inputBinding": { | |
| "position": 2, | |
| "prefix": "-R" | |
| }, | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".pac", | |
| ".sa", | |
| ".fai", | |
| "^.dict" | |
| ], | |
| "id": "#GATK4-BaseRecalibrator.cwl/reference" | |
| }, | |
| { | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "--use-original-qualities" | |
| }, | |
| "id": "#GATK4-BaseRecalibrator.cwl/use_original_qualities" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.output_recalibration_report_filename)" | |
| }, | |
| "id": "#GATK4-BaseRecalibrator.cwl/output_recalibration_report" | |
| } | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "BaseRecalibrator", | |
| "position": 0 | |
| } | |
| ], | |
| "id": "#GATK4-BaseRecalibrator.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "broadinstitute/gatk:4.0.4.0" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "hints": [ | |
| { | |
| "class": "SoftwareRequirement", | |
| "packages": [ | |
| { | |
| "version": [ | |
| "4.0.4.0" | |
| ], | |
| "https://schema.org/citation": "https://doi.org/10.1101/gr.107524.110", | |
| "package": "gatk" | |
| } | |
| ] | |
| } | |
| ], | |
| "baseCommand": "gatk", | |
| "inputs": [ | |
| { | |
| "type": [ | |
| "null", | |
| { | |
| "type": "array", | |
| "items": "string", | |
| "inputBinding": { | |
| "prefix": "-G" | |
| } | |
| } | |
| ], | |
| "doc": "One or more groups of annotations to apply to variant calls This argument may be specified 0 or more times. Default value: [StandardAnnotation, StandardHCAnnotation].", | |
| "id": "#GATK4-HaplotypeCaller.cwl/annotation_groups" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "File" | |
| ], | |
| "inputBinding": { | |
| "prefix": "-D" | |
| }, | |
| "secondaryFiles": [ | |
| ".idx" | |
| ], | |
| "doc": "dbSNP file. Default value: null", | |
| "id": "#GATK4-HaplotypeCaller.cwl/dbsnp" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "inputBinding": { | |
| "prefix": "-ERC" | |
| }, | |
| "doc": "Mode for emitting reference confidence scores Default value: NONE. Possible values: {NONE, BP_RESOLUTION, GVCF}", | |
| "id": "#GATK4-HaplotypeCaller.cwl/emit_ref_confidence" | |
| }, | |
| { | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "-I" | |
| }, | |
| "secondaryFiles": [ | |
| "^.bai" | |
| ], | |
| "doc": "BAM/SAM/CRAM file containing reads. Required.", | |
| "id": "#GATK4-HaplotypeCaller.cwl/input_bam" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "int" | |
| ], | |
| "doc": "Amount of padding (in bp) to add to each interval you are including. Defaults to 0", | |
| "inputBinding": { | |
| "prefix": "-ip" | |
| }, | |
| "id": "#GATK4-HaplotypeCaller.cwl/interval_padding" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| { | |
| "type": "array", | |
| "items": "File", | |
| "inputBinding": { | |
| "prefix": "-L" | |
| } | |
| } | |
| ], | |
| "doc": "One or more genomic intervals over which to operate", | |
| "id": "#GATK4-HaplotypeCaller.cwl/intervals" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "String of options to pass to JVM at runtime", | |
| "inputBinding": { | |
| "prefix": "--java-options", | |
| "position": -1, | |
| "shellQuote": true | |
| }, | |
| "id": "#GATK4-HaplotypeCaller.cwl/java_opt" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "inputBinding": { | |
| "prefix": "-bamout" | |
| }, | |
| "doc": "File to which assembled haplotypes should be written.", | |
| "id": "#GATK4-HaplotypeCaller.cwl/output_bam_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "inputBinding": { | |
| "prefix": "-O" | |
| }, | |
| "doc": "File to which variants should be written Required. Use .g.vcf to make a GVCF file.", | |
| "id": "#GATK4-HaplotypeCaller.cwl/output_variants_filename" | |
| }, | |
| { | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "-R" | |
| }, | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".pac", | |
| ".sa", | |
| ".fai", | |
| "^.dict" | |
| ], | |
| "doc": "Reference sequence file Required.", | |
| "id": "#GATK4-HaplotypeCaller.cwl/reference" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.output_bam_filename)" | |
| }, | |
| "secondaryFiles": [ | |
| "^.bai" | |
| ], | |
| "id": "#GATK4-HaplotypeCaller.cwl/output_bam" | |
| }, | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.output_variants_filename)" | |
| }, | |
| "secondaryFiles": [ | |
| ".idx" | |
| ], | |
| "id": "#GATK4-HaplotypeCaller.cwl/output_variants" | |
| } | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "HaplotypeCaller", | |
| "position": 0 | |
| } | |
| ], | |
| "id": "#GATK4-HaplotypeCaller.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "broadinstitute/gatk:4.0.4.0" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "hints": [ | |
| { | |
| "class": "SoftwareRequirement", | |
| "packages": [ | |
| { | |
| "version": [ | |
| "4.0.4.0" | |
| ], | |
| "https://schema.org/citation": "https://doi.org/10.1101/gr.107524.110", | |
| "package": "gatk" | |
| } | |
| ] | |
| } | |
| ], | |
| "baseCommand": "gatk", | |
| "inputs": [ | |
| { | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "inputBinding": { | |
| "prefix": "--ASSUME_SORT_ORDER" | |
| }, | |
| "id": "#GATK4-MarkDuplicates.cwl/assume_sort_order" | |
| }, | |
| { | |
| "type": "string", | |
| "default": "false", | |
| "inputBinding": { | |
| "prefix": "--CREATE_INDEX" | |
| }, | |
| "doc": "Create an index", | |
| "id": "#GATK4-MarkDuplicates.cwl/create_index" | |
| }, | |
| { | |
| "type": "File", | |
| "doc": "One or more input SAM or BAM files to analyze. Must be coordinate sorted.", | |
| "inputBinding": { | |
| "prefix": "--INPUT" | |
| }, | |
| "id": "#GATK4-MarkDuplicates.cwl/input_file" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "doc": "String of options to pass to JVM at runtime", | |
| "inputBinding": { | |
| "prefix": "--java-options", | |
| "position": -1, | |
| "shellQuote": true | |
| }, | |
| "id": "#GATK4-MarkDuplicates.cwl/java_opt" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Output metrics filename", | |
| "default": "marked_dup_metrics.txt", | |
| "inputBinding": { | |
| "prefix": "--METRICS_FILE" | |
| }, | |
| "id": "#GATK4-MarkDuplicates.cwl/metrics_filename" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "int" | |
| ], | |
| "inputBinding": { | |
| "prefix": "--OPTICAL_DUPLICATE_PIXEL_DISTANCE" | |
| }, | |
| "id": "#GATK4-MarkDuplicates.cwl/optical_duplicate_pixel_distance" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Output filename", | |
| "default": "marked_duplicates.bam", | |
| "inputBinding": { | |
| "prefix": "--OUTPUT" | |
| }, | |
| "id": "#GATK4-MarkDuplicates.cwl/output_filename" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "doc": "If true do not write duplicates to the output file instead of writing them with appropriate flags set. (Default true).", | |
| "inputBinding": { | |
| "prefix": "--REMOVE_DUPLICATES:", | |
| "shellQuote": false | |
| }, | |
| "id": "#GATK4-MarkDuplicates.cwl/remove_duplicates" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "inputBinding": { | |
| "prefix": "--VALIDATION_STRINGENCY" | |
| }, | |
| "id": "#GATK4-MarkDuplicates.cwl/validation_stringency" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.output_filename)" | |
| }, | |
| "secondaryFiles": [ | |
| "^.bai" | |
| ], | |
| "id": "#GATK4-MarkDuplicates.cwl/output_dedup_bam_file" | |
| }, | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.metrics_filename)" | |
| }, | |
| "id": "#GATK4-MarkDuplicates.cwl/output_metrics_file" | |
| } | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "MarkDuplicates", | |
| "position": 0 | |
| } | |
| ], | |
| "id": "#GATK4-MarkDuplicates.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "broadinstitute/gatk:4.0.4.0" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "hints": [ | |
| { | |
| "class": "SoftwareRequirement", | |
| "packages": [ | |
| { | |
| "version": [ | |
| "4.0.4.0" | |
| ], | |
| "https://schema.org/citation": "https://doi.org/10.1101/gr.107524.110", | |
| "package": "gatk" | |
| } | |
| ] | |
| } | |
| ], | |
| "baseCommand": "gatk", | |
| "inputs": [ | |
| { | |
| "type": "string", | |
| "default": "false", | |
| "inputBinding": { | |
| "prefix": "--CREATE_INDEX" | |
| }, | |
| "doc": "Create an index", | |
| "id": "#GATK4-SortSam.cwl/create_index" | |
| }, | |
| { | |
| "type": "File", | |
| "doc": "One or more input SAM or BAM files to sort", | |
| "inputBinding": { | |
| "prefix": "--INPUT" | |
| }, | |
| "id": "#GATK4-SortSam.cwl/input_file" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "doc": "String of options to pass to JVM at runtime", | |
| "inputBinding": { | |
| "prefix": "--java-options", | |
| "position": -1, | |
| "shellQuote": true | |
| }, | |
| "id": "#GATK4-SortSam.cwl/java_opt" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Output filename", | |
| "default": "sorted.bam", | |
| "inputBinding": { | |
| "prefix": "--OUTPUT" | |
| }, | |
| "id": "#GATK4-SortSam.cwl/output_sorted_bam_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Sort order (e.g. coordinate)", | |
| "inputBinding": { | |
| "prefix": "--SORT_ORDER" | |
| }, | |
| "id": "#GATK4-SortSam.cwl/sort_order" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.output_sorted_bam_filename)" | |
| }, | |
| "secondaryFiles": [ | |
| "^.bai" | |
| ], | |
| "id": "#GATK4-SortSam.cwl/output_sorted_bam" | |
| } | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "SortSam", | |
| "position": 0 | |
| } | |
| ], | |
| "id": "#GATK4-SortSam.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "requirements": [ | |
| { | |
| "class": "InitialWorkDirRequirement", | |
| "listing": [ | |
| { | |
| "entryname": "combinefiles.sh", | |
| "entry": "zcat \"$@\" | gzip\n" | |
| } | |
| ] | |
| } | |
| ], | |
| "baseCommand": "bash", | |
| "arguments": [ | |
| "combinefiles.sh" | |
| ], | |
| "inputs": [ | |
| { | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| }, | |
| "inputBinding": { | |
| "position": 2, | |
| "shellQuote": false | |
| }, | |
| "id": "#concat-gz-files.cwl/files" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#concat-gz-files.cwl/output_filename" | |
| } | |
| ], | |
| "stdout": "$(inputs.output_filename)", | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.output_filename)" | |
| }, | |
| "id": "#concat-gz-files.cwl/output" | |
| } | |
| ], | |
| "id": "#concat-gz-files.cwl" | |
| }, | |
| { | |
| "class": "ExpressionTool", | |
| "label": "Given a FASTQReadPairType returns a 2D array of the files contained within", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "$import": "#bespin-types.yml" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "type": "string", | |
| "id": "#extract-named-file-pair-details.cwl/library" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#extract-named-file-pair-details.cwl/platform" | |
| }, | |
| { | |
| "type": "#bespin-types.yml/FASTQReadPairType", | |
| "id": "#extract-named-file-pair-details.cwl/read_pair" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": "string", | |
| "id": "#extract-named-file-pair-details.cwl/read_group_header" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#extract-named-file-pair-details.cwl/read_pair_name" | |
| }, | |
| { | |
| "type": { | |
| "type": "array", | |
| "items": { | |
| "type": "array", | |
| "items": "File" | |
| } | |
| }, | |
| "id": "#extract-named-file-pair-details.cwl/reads" | |
| } | |
| ], | |
| "expression": "${\n var readPairName = inputs.read_pair.name;\n var readGroupHeader = \"@RG\" +\n \"\\\\tID:\" + readPairName +\n \"\\\\tLB:\" + inputs.library +\n \"\\\\tPL:\" + inputs.platform +\n \"\\\\tPU:\" + readPairName +\n \"\\\\tSM:\" + readPairName;\n return {\n reads: [\n inputs.read_pair.read1_files,\n inputs.read_pair.read2_files,\n ],\n read_pair_name: readPairName,\n read_group_header: readGroupHeader\n };\n\n}\n", | |
| "id": "#extract-named-file-pair-details.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "hints": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "dukegcb/fastqc:0.11.4" | |
| }, | |
| { | |
| "class": "SoftwareRequirement", | |
| "packages": [ | |
| { | |
| "version": [ | |
| "0.11.4" | |
| ], | |
| "package": "fastqc", | |
| "https://schema.org/citation": "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" | |
| } | |
| ] | |
| } | |
| ], | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "type": "string", | |
| "default": "fastq", | |
| "inputBinding": { | |
| "position": 3, | |
| "prefix": "--format" | |
| }, | |
| "id": "#fastqc.cwl/format" | |
| }, | |
| { | |
| "type": "File", | |
| "inputBinding": { | |
| "position": 4 | |
| }, | |
| "id": "#fastqc.cwl/input_fastq_file" | |
| }, | |
| { | |
| "type": "boolean", | |
| "default": true, | |
| "inputBinding": { | |
| "prefix": "--noextract", | |
| "position": 2 | |
| }, | |
| "id": "#fastqc.cwl/noextract" | |
| }, | |
| { | |
| "type": "int", | |
| "default": 1, | |
| "doc": "The number of threads to use. The fastqc wrapper script requests 250MB of memory per thread, so keep this in line with any CWL ResourceRequirement", | |
| "inputBinding": { | |
| "position": 5, | |
| "prefix": "--threads" | |
| }, | |
| "id": "#fastqc.cwl/threads" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "*_fastqc.zip" | |
| }, | |
| "id": "#fastqc.cwl/output_qc_report" | |
| } | |
| ], | |
| "baseCommand": "fastqc", | |
| "arguments": [ | |
| { | |
| "valueFrom": "$('/tmp')", | |
| "prefix": "--dir", | |
| "position": 5 | |
| }, | |
| { | |
| "valueFrom": "$(runtime.outdir)", | |
| "prefix": "-o", | |
| "position": 5 | |
| } | |
| ], | |
| "id": "#fastqc.cwl" | |
| }, | |
| { | |
| "class": "ExpressionTool", | |
| "label": "Generates a set of file names for preprocessing steps based on an input sample name", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/sample_name" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": { | |
| "type": "array", | |
| "items": "string" | |
| }, | |
| "id": "#generate-sample-filenames.cwl/combined_reads_output_filenames" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/dedup_metrics_output_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/dedup_reads_output_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/fixedtag_reads_output_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/haplotypes_bam_output_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/hs_metrics_output_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/mapped_reads_output_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/raw_variants_output_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/recal_reads_output_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/recal_table_output_filename" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#generate-sample-filenames.cwl/sorted_reads_output_filename" | |
| } | |
| ], | |
| "expression": "${\n function makeFilename(base, suffix, extension) {\n return base + '-' + suffix + '.' + extension;\n }\n var base = inputs.sample_name\n\n return {\n combined_reads_output_filenames: [\n makeFilename(base, 'R1', 'fastq.gz'),\n makeFilename(base, 'R2', 'fastq.gz'),\n ],\n mapped_reads_output_filename: makeFilename(base, 'mapped', 'bam'),\n sorted_reads_output_filename: makeFilename(base, 'sorted', 'bam'),\n dedup_reads_output_filename: makeFilename(base, 'dedup', 'bam'),\n dedup_metrics_output_filename: makeFilename(base, 'dedup-metrics', 'out'),\n recal_reads_output_filename: makeFilename(base, 'recal', 'bam'),\n recal_table_output_filename: makeFilename(base, 'recal', 'table'),\n raw_variants_output_filename: makeFilename(base, 'raw_variants', 'g.vcf'),\n haplotypes_bam_output_filename: makeFilename(base, 'haplotypes', 'bam'),\n hs_metrics_output_filename: makeFilename(base, 'hs', 'txt'),\n fixedtag_reads_output_filename: makeFilename(base, 'fixed_tags', 'bam')\n };\n}\n", | |
| "id": "#generate-sample-filenames.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "broadinstitute/genomes-in-the-cloud:2.3.1-1512499786" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "InitialWorkDirRequirement", | |
| "listing": [ | |
| { | |
| "entryname": "bwa-mem-samtools.sh", | |
| "entry": "/usr/gitc/bwa mem $@ | samtools view -1 -\n" | |
| } | |
| ] | |
| } | |
| ], | |
| "baseCommand": "bash", | |
| "arguments": [ | |
| "bwa-mem-samtools.sh" | |
| ], | |
| "hints": [ | |
| { | |
| "class": "SoftwareRequirement", | |
| "packages": [ | |
| { | |
| "version": [ | |
| "0.7.15" | |
| ], | |
| "package": "bwa", | |
| "https://schema.org/citation": "https://dx.doi.org/10.1093/bioinformatics/btp324" | |
| }, | |
| { | |
| "version": [ | |
| "1.3.1" | |
| ], | |
| "package": "samtools", | |
| "https://schema.org/citation": "https://doi.org/10.1093/bioinformatics/btp352" | |
| } | |
| ] | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "type": [ | |
| "null", | |
| { | |
| "type": "array", | |
| "items": "int" | |
| } | |
| ], | |
| "inputBinding": { | |
| "position": 1, | |
| "prefix": "-I", | |
| "itemSeparator": "," | |
| }, | |
| "id": "#gitc-bwa-mem-samtools.cwl/min_std_max_min" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "int" | |
| ], | |
| "inputBinding": { | |
| "position": 1, | |
| "prefix": "-k" | |
| }, | |
| "doc": "-k INT minimum seed length [19]", | |
| "id": "#gitc-bwa-mem-samtools.cwl/minimum_seed_length" | |
| }, | |
| { | |
| "type": "string", | |
| "id": "#gitc-bwa-mem-samtools.cwl/output_filename" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "inputBinding": { | |
| "position": 1, | |
| "prefix": "-R" | |
| }, | |
| "doc": "-R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]", | |
| "id": "#gitc-bwa-mem-samtools.cwl/read_group_header" | |
| }, | |
| { | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| }, | |
| "inputBinding": { | |
| "position": 3 | |
| }, | |
| "id": "#gitc-bwa-mem-samtools.cwl/reads" | |
| }, | |
| { | |
| "type": "File", | |
| "inputBinding": { | |
| "position": 2 | |
| }, | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".pac", | |
| ".sa" | |
| ], | |
| "id": "#gitc-bwa-mem-samtools.cwl/reference" | |
| }, | |
| { | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "-p" | |
| }, | |
| "doc": "smart pairing (ignoring in2.fq)", | |
| "id": "#gitc-bwa-mem-samtools.cwl/smart_pairing" | |
| }, | |
| { | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "-Y" | |
| }, | |
| "id": "#gitc-bwa-mem-samtools.cwl/soft_clipping" | |
| }, | |
| { | |
| "type": "int", | |
| "inputBinding": { | |
| "position": 1, | |
| "prefix": "-t" | |
| }, | |
| "doc": "-t INT number of threads [1]", | |
| "id": "#gitc-bwa-mem-samtools.cwl/threads" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "int" | |
| ], | |
| "inputBinding": { | |
| "prefix": "-v" | |
| }, | |
| "doc": "verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]", | |
| "id": "#gitc-bwa-mem-samtools.cwl/verbosity" | |
| } | |
| ], | |
| "stdout": "$(inputs.output_filename)", | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.output_filename)" | |
| }, | |
| "id": "#gitc-bwa-mem-samtools.cwl/output" | |
| } | |
| ], | |
| "id": "#gitc-bwa-mem-samtools.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "dukegcb/picard:2.10.7" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "hints": [ | |
| { | |
| "class": "SoftwareRequirement", | |
| "packages": [ | |
| { | |
| "version": [ | |
| "2.10.7" | |
| ], | |
| "package": "picard", | |
| "https://schema.org/citation": "http://broadinstitute.github.io/picard" | |
| } | |
| ] | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "type": [ | |
| "null", | |
| { | |
| "type": "array", | |
| "items": "File" | |
| } | |
| ], | |
| "doc": "The bed file to be converted to interval_list format. Required.", | |
| "inputBinding": { | |
| "prefix": "I=", | |
| "shellQuote": false | |
| }, | |
| "id": "#picard-BedToIntervalList.cwl/input_file" | |
| }, | |
| { | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "doc": "Interval list output filename.", | |
| "default": "list.interval_list", | |
| "inputBinding": { | |
| "prefix": "O=", | |
| "shellQuote": false | |
| }, | |
| "id": "#picard-BedToIntervalList.cwl/output_filename" | |
| }, | |
| { | |
| "type": "File", | |
| "doc": "The reference sequences in fasta format.", | |
| "inputBinding": { | |
| "prefix": "SD=", | |
| "shellQuote": false | |
| }, | |
| "id": "#picard-BedToIntervalList.cwl/reference_sequence" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.output_filename)" | |
| }, | |
| "id": "#picard-BedToIntervalList.cwl/output_interval_list_file" | |
| } | |
| ], | |
| "baseCommand": [ | |
| "java", | |
| "-Xmx4g" | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "/opt/picard/picard.jar", | |
| "position": -1, | |
| "prefix": "-jar" | |
| }, | |
| { | |
| "valueFrom": "BedToIntervalList", | |
| "position": 0 | |
| } | |
| ], | |
| "id": "#picard-BedToIntervalList.cwl" | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "hints": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "dukegcb/trim-galore:0.4.4" | |
| }, | |
| { | |
| "class": "SoftwareRequirement", | |
| "packages": [ | |
| { | |
| "version": [ | |
| "1.14" | |
| ], | |
| "package": "cutadapt", | |
| "https://schema.org/citation": "https://dx.doi.org/10.14806/ej.17.1.200" | |
| }, | |
| { | |
| "version": [ | |
| "0.4.4" | |
| ], | |
| "package": "trimgalore", | |
| "https://schema.org/citation": "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/" | |
| } | |
| ] | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "type": "boolean", | |
| "inputBinding": { | |
| "position": 1, | |
| "prefix": "--paired" | |
| }, | |
| "id": "#trim_galore.cwl/paired" | |
| }, | |
| { | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| }, | |
| "inputBinding": { | |
| "position": 3 | |
| }, | |
| "id": "#trim_galore.cwl/reads" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| }, | |
| "outputBinding": { | |
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| }, | |
| "id": "#trim_galore.cwl/trim_reports" | |
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| ], | |
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| "valueFrom": "$(runtime.outdir)", | |
| "prefix": "-o", | |
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| ], | |
| "id": "#trim_galore.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "label": "WES GATK4 Preprocessing", | |
| "doc": "Whole Exome Sequence analysis GATK4 Preprocessing\n", | |
| "requirements": [ | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SubworkflowFeatureRequirement" | |
| }, | |
| { | |
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| } | |
| ], | |
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| { | |
| "type": [ | |
| "null", | |
| { | |
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| "items": "File" | |
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| ], | |
| "id": "#main/bait_intervals" | |
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| { | |
| "type": [ | |
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| "id": "#main/interval_padding" | |
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| "id": "#main/haplotypes_bam" | |
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| "outputSource": "#main/preprocessing/trim_reports", | |
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| "id": "#main/prepare_reference_data/reference_genome" | |
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| "id": "#main/prepare_reference_data/target_intervals" | |
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| "id": "#main/prepare_reference_data" | |
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| { | |
| "run": "#exomeseq-gatk4-01-preprocessing.cwl", | |
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| "source": "#main/prepare_reference_data/bait_interval_list", | |
| "id": "#main/preprocessing/bait_interval_list" | |
| }, | |
| { | |
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| "id": "#main/preprocessing/interval_padding" | |
| }, | |
| { | |
| "source": "#main/target_intervals", | |
| "id": "#main/preprocessing/intervals" | |
| }, | |
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| "id": "#main/preprocessing/known_sites" | |
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| { | |
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| { | |
| "source": "#main/platform", | |
| "id": "#main/preprocessing/platform" | |
| }, | |
| { | |
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| "id": "#main/preprocessing/read_pair" | |
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| { | |
| "source": "#main/reference_genome", | |
| "id": "#main/preprocessing/reference_genome" | |
| }, | |
| { | |
| "source": "#main/resource_dbsnp", | |
| "id": "#main/preprocessing/resource_dbsnp" | |
| }, | |
| { | |
| "source": "#main/prepare_reference_data/target_interval_list", | |
| "id": "#main/preprocessing/target_interval_list" | |
| }, | |
| { | |
| "source": "#main/threads", | |
| "id": "#main/preprocessing/threads" | |
| } | |
| ], | |
| "out": [ | |
| "#main/preprocessing/fastqc_reports", | |
| "#main/preprocessing/trim_reports", | |
| "#main/preprocessing/markduplicates_bam", | |
| "#main/preprocessing/recalibration_table", | |
| "#main/preprocessing/recalibrated_reads", | |
| "#main/preprocessing/raw_variants", | |
| "#main/preprocessing/haplotypes_bam" | |
| ], | |
| "id": "#main/preprocessing" | |
| } | |
| ], | |
| "id": "#main" | |
| } | |
| ], | |
| "cwlVersion": "v1.0", | |
| "$schemas": [ | |
| "https://schema.org/docs/schema_org_rdfa.html" | |
| ] | |
| } |
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