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dleehr/exomeseq-gatk4.cwl

Created December 6, 2018 20:41
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exomeseq-gatk4.cwl
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{
"source": "#exomeseq-gatk4-01-preprocessing.cwl/reference_genome",
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},
{
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],
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{
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],
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},
{
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],
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{
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{
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}
],
"id": "#exomeseq-gatk4-01-preprocessing.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"types": [
{
"type": "enum",
"name": "#ExomeseqStudyType.yml/ExomeseqStudyType",
"label": "The type of study",
"symbols": [
"#ExomeseqStudyType.yml/ExomeseqStudyType/Small Familial",
"#ExomeseqStudyType.yml/ExomeseqStudyType/Large Population"
],
"id": "#ExomeseqStudyType.yml"
}
],
"class": "SchemaDefRequirement"
}
],
"inputs": [
{
"type": "File",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/indel_resource_mills"
},
{
"type": [
"null",
"int"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/interval_padding"
},
{
"type": [
"null",
{
"type": "array",
"items": "File"
}
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/intervals"
},
{
"type": "string",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/name"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/raw_variants"
},
{
"type": "File",
"secondaryFiles": [
".amb",
".ann",
".bwt",
".pac",
".sa",
".fai",
"^.dict"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/reference_genome"
},
{
"type": "File",
"secondaryFiles": [
".idx"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/resource_dbsnp"
},
{
"type": "File",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/snp_resource_1kg"
},
{
"type": "File",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/snp_resource_hapmap"
},
{
"type": "File",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/snp_resource_omni"
},
{
"type": "#ExomeseqStudyType.yml/ExomeseqStudyType",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/study_type"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/output_detail_metrics",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/detail_metrics"
},
{
"type": "File",
"outputSource": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/output_vcf",
"doc": "VCF file from joint genotyping calling",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_raw_variants"
},
{
"type": "File",
"outputSource": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/output_summary_metrics",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/summary_metrics"
},
{
"type": "File",
"outputSource": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/output_recalibrated_variants",
"doc": "The output VCF file after INDEL and SNP recalibration",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_combined_vcf"
},
{
"type": "File",
"outputSource": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_tranches",
"doc": "The output tranches file used by ApplyVQSR in INDEL mode",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels_tranches"
},
{
"type": "File",
"outputSource": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/output_recalibrated_variants",
"doc": "The output VCF file after INDEL recalibration",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels_vcf"
},
{
"type": "File",
"outputSource": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_recalibration",
"doc": "The output recalibration file used by ApplyVQSR in INDEL mode",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps_indels_recalibration"
},
{
"type": "File",
"outputSource": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/output_recalibration",
"doc": "The output recalibration file used by ApplyVQSR in SNP mode",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps_recalibration"
},
{
"type": "File",
"outputSource": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/output_tranches",
"doc": "The output tranches file used by ApplyVQSR in SNP mode",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps_tranches"
}
],
"steps": [
{
"run": "#GATK4-ApplyVQSR.cwl",
"requirements": [
{
"class": "ResourceRequirement",
"coresMin": 1,
"ramMin": 7168
}
],
"in": [
{
"default": true,
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/create_output_variant_index"
},
{
"default": "-Xmx5g -Xms5g",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/java_opt"
},
{
"default": "INDEL",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/mode"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/indels_recalibrated_variants_filename",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/output_recalibrated_variants_filename"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_recalibration",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/recalibration_file"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_tranches",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/tranches_file"
},
{
"default": 99.7,
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/truth_sensitivity_filter_level"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/output_vcf",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/variants"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/output_recalibrated_variants"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels"
},
{
"run": "#GATK4-ApplyVQSR.cwl",
"requirements": [
{
"class": "ResourceRequirement",
"coresMin": 1,
"ramMin": 7168
}
],
"in": [
{
"default": true,
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/create_output_variant_index"
},
{
"default": "-Xmx5g -Xms5g",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/java_opt"
},
{
"default": "SNP",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/mode"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/combined_recalibrated_variants_filename",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/output_recalibrated_variants_filename"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_recalibration",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/recalibration_file"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_tranches",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/tranches_file"
},
{
"default": 99.7,
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/truth_sensitivity_filter_level"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_indels/output_recalibrated_variants",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/variants"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/output_recalibrated_variants"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps"
},
{
"run": "#GATK4-CollectVariantCallingMetrics.cwl",
"requirements": [
{
"class": "ResourceRequirement",
"coresMin": 2,
"ramMin": 7168
}
],
"in": [
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/resource_dbsnp",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/dbsnp"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/apply_vqsr_snps/output_recalibrated_variants",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/input_vcf"
},
{
"default": "-Xmx6g -Xms6g",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/java_opt"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/name",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/output_metrics_filename_prefix"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/extract_sequence_dict/extracted",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/sequence_dictionary"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/extract_intervals_file/extracted",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/target_intervals"
},
{
"default": 8,
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/thread_count"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/output_detail_metrics",
"#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics/output_summary_metrics"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/collect_metrics"
},
{
"run": "#extract-array-file.cwl",
"in": [
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/intervals",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/extract_intervals_file/files"
},
{
"default": 0,
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/extract_intervals_file/index"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/extract_intervals_file/extracted"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/extract_intervals_file"
},
{
"run": "#extract-secondary-file.cwl",
"in": [
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/reference_genome",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/extract_sequence_dict/file"
},
{
"default": ".dict",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/extract_sequence_dict/pattern"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/extract_sequence_dict/extracted"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/extract_sequence_dict"
},
{
"run": "#generate-variant-recalibration-annotation-set.cwl",
"in": [
{
"default": [
"FS",
"ReadPosRankSum",
"MQRankSum",
"QD",
"SOR",
"DP"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_indels/base_annotations"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/study_type",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_indels/study_type"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_indels/annotations"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_indels"
},
{
"run": "#generate-variant-recalibration-annotation-set.cwl",
"in": [
{
"default": [
"QD",
"MQRankSum",
"ReadPosRankSum",
"FS",
"MQ",
"SOR",
"DP"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_snps/base_annotations"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/study_type",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_snps/study_type"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_snps/annotations"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_snps"
},
{
"run": "#generate-joint-filenames.cwl",
"in": [
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/name",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/name"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/raw_variants_filename",
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/snps_recalibration_filename",
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/snps_tranches_filename",
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/snps_recalibrated_variants_filename",
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/indels_recalibration_filename",
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/indels_tranches_filename",
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/indels_recalibrated_variants_filename",
"#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/combined_recalibrated_variants_filename"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames"
},
{
"run": "#GATK4-GenotypeGVCFs.cwl",
"requirements": [
{
"class": "ResourceRequirement",
"coresMin": 2,
"ramMin": 7168
}
],
"in": [
{
"default": [
"StandardAnnotation",
"AS_StandardAnnotation"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/annotation_groups"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/resource_dbsnp",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/dbsnp"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/interval_padding",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/interval_padding"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/intervals",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/intervals"
},
{
"default": "-Xmx5g -Xms5g",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/java_opt"
},
{
"default": true,
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/only_output_calls_starting_in_intervals"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/raw_variants_filename",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/output_vcf_filename"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/reference_genome",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/reference"
},
{
"default": true,
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/use_new_qual_calculator"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/raw_variants",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/variants"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/output_vcf"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping"
},
{
"run": "#GATK4-VariantRecalibrator.cwl",
"requirements": [
{
"class": "ResourceRequirement",
"coresMin": 2,
"ramMin": 26624
}
],
"in": [
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_snps/annotations",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/annotations"
},
{
"default": "-Xmx24g -Xms24g",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/java_opt"
},
{
"default": "SNP",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/mode"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/indels_recalibration_filename",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_recalibration_filename"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/indels_tranches_filename",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_tranches_filename"
},
{
"default": [
{
"name": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/resources/mills",
"known": false,
"training": true,
"truth": true,
"prior": 12,
"file": "indel_resource_mills"
},
{
"name": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/resources/dbsnp",
"known": true,
"training": false,
"truth": false,
"prior": 2,
"file": "resource_dbsnp"
}
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/resources"
},
{
"default": [
"100.0",
"99.95",
"99.9",
"99.8",
"99.6",
"99.5",
"99.4",
"99.3",
"99.0",
"98.0",
"97.0",
"90.0"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/tranches"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/output_vcf",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/variants"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_recalibration",
"#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels/output_tranches"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_indels"
},
{
"run": "#GATK4-VariantRecalibrator.cwl",
"requirements": [
{
"class": "ResourceRequirement",
"coresMin": 2,
"ramMin": 4096
}
],
"in": [
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_annotations_snps/annotations",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/annotations"
},
{
"default": "-Xmx3g -Xms3g",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/java_opt"
},
{
"default": "SNP",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/mode"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/snps_recalibration_filename",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/output_recalibration_filename"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/generate_joint_filenames/snps_tranches_filename",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/output_tranches_filename"
},
{
"default": [
{
"name": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/resources/hapmap",
"known": false,
"training": true,
"truth": true,
"prior": 15,
"file": "snp_resource_hapmap"
},
{
"name": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/resources/omni",
"known": false,
"training": true,
"truth": true,
"prior": 12,
"file": "snp_resource_omni"
},
{
"name": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/resources/1000G",
"known": false,
"training": true,
"truth": false,
"prior": 10,
"file": "snp_resource_1kg"
},
{
"name": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/resources/dbsnp",
"known": true,
"training": false,
"truth": false,
"prior": 7,
"file": "resource_dbsnp"
}
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/resources"
},
{
"default": [
"100.0",
"99.95",
"99.9",
"99.8",
"99.6",
"99.5",
"99.4",
"99.3",
"99.0",
"98.0",
"97.0",
"90.0"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/tranches"
},
{
"source": "#exomeseq-gatk4-02-variantdiscovery.cwl/joint_genotyping/output_vcf",
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/variants"
}
],
"out": [
"#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/output_recalibration",
"#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps/output_tranches"
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl/variant_recalibration_snps"
}
],
"id": "#exomeseq-gatk4-02-variantdiscovery.cwl"
},
{
"class": "Workflow",
"inputs": [
{
"type": {
"type": "array",
"items": "File"
},
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/bams_markduplicates"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/bams_recalibrated"
},
{
"type": {
"type": "array",
"items": {
"type": "array",
"items": "File"
}
},
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/fastqc_reports"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/raw_variants"
},
{
"type": {
"type": "array",
"items": {
"type": "array",
"items": "File"
}
},
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/trim_reports"
}
],
"outputs": [
{
"type": "Directory",
"outputSource": "#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_markduplicates/outdir",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/bams_markduplicates_dir"
},
{
"type": "Directory",
"outputSource": "#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_recalibrated/outdir",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/bams_recalibrated_dir"
},
{
"type": "Directory",
"outputSource": "#exomeseq-gatk4-03-organizedirectories.cwl/org_fastqc_reports/outdir",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/fastqc_reports_dir"
},
{
"type": "Directory",
"outputSource": "#exomeseq-gatk4-03-organizedirectories.cwl/org_raw_variants/outdir",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/raw_variants_dir"
},
{
"type": "Directory",
"outputSource": "#exomeseq-gatk4-03-organizedirectories.cwl/org_trim_reports/outdir",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/trim_reports_dir"
}
],
"steps": [
{
"run": "#files-to-directory.cwl",
"in": [
{
"source": "#exomeseq-gatk4-03-organizedirectories.cwl/bams_markduplicates",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_markduplicates/files"
},
{
"default": "bams-markduplicates",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_markduplicates/name"
}
],
"out": [
"#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_markduplicates/outdir"
],
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_markduplicates"
},
{
"run": "#files-to-directory.cwl",
"in": [
{
"source": "#exomeseq-gatk4-03-organizedirectories.cwl/bams_recalibrated",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_recalibrated/files"
},
{
"default": "bams-recalibrated",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_recalibrated/name"
}
],
"out": [
"#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_recalibrated/outdir"
],
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_bams_recalibrated"
},
{
"run": "#file-pairs-to-directory.cwl",
"in": [
{
"source": "#exomeseq-gatk4-03-organizedirectories.cwl/fastqc_reports",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_fastqc_reports/file_pairs"
},
{
"default": "fastqc-reports",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_fastqc_reports/name"
}
],
"out": [
"#exomeseq-gatk4-03-organizedirectories.cwl/org_fastqc_reports/outdir"
],
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_fastqc_reports"
},
{
"run": "#files-to-directory.cwl",
"in": [
{
"source": "#exomeseq-gatk4-03-organizedirectories.cwl/raw_variants",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_raw_variants/files"
},
{
"default": "gvcfs",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_raw_variants/name"
}
],
"out": [
"#exomeseq-gatk4-03-organizedirectories.cwl/org_raw_variants/outdir"
],
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_raw_variants"
},
{
"run": "#file-pairs-to-directory.cwl",
"in": [
{
"source": "#exomeseq-gatk4-03-organizedirectories.cwl/trim_reports",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_trim_reports/file_pairs"
},
{
"default": "trim-reports",
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_trim_reports/name"
}
],
"out": [
"#exomeseq-gatk4-03-organizedirectories.cwl/org_trim_reports/outdir"
],
"id": "#exomeseq-gatk4-03-organizedirectories.cwl/org_trim_reports"
}
],
"id": "#exomeseq-gatk4-03-organizedirectories.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": [
"null",
"boolean"
],
"inputBinding": {
"prefix": "--create-output-variant-index",
"position": 5
},
"doc": "Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation. Default value: false.",
"id": "#GATK4-ApplyVQSR.cwl/create_output_variant_index"
},
{
"type": "string",
"doc": "String of options to pass to JVM at runtime",
"inputBinding": {
"prefix": "--java-options",
"position": -1,
"shellQuote": true
},
"id": "#GATK4-ApplyVQSR.cwl/java_opt"
},
{
"type": {
"type": "enum",
"symbols": [
"#GATK4-ApplyVQSR.cwl/mode/SNP",
"#GATK4-ApplyVQSR.cwl/mode/INDEL",
"#GATK4-ApplyVQSR.cwl/mode/BOTH"
]
},
"inputBinding": {
"prefix": "-mode",
"position": 7
},
"doc": "Recalibration mode to employ Default value: SNP. Possible values: {SNP, INDEL, BOTH}",
"id": "#GATK4-ApplyVQSR.cwl/mode"
},
{
"type": "string",
"inputBinding": {
"prefix": "-O",
"position": 1
},
"doc": "The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value Required",
"id": "#GATK4-ApplyVQSR.cwl/output_recalibrated_variants_filename"
},
{
"type": "File",
"inputBinding": {
"prefix": "--recal-file",
"position": 2
},
"doc": "The input recal file used by ApplyRecalibration Required.",
"id": "#GATK4-ApplyVQSR.cwl/recalibration_file"
},
{
"type": [
"null",
"File"
],
"inputBinding": {
"prefix": "--tranches-file",
"position": 3
},
"doc": "The input tranches file describing where to cut the data",
"id": "#GATK4-ApplyVQSR.cwl/tranches_file"
},
{
"type": [
"null",
"float"
],
"inputBinding": {
"prefix": "--truth-sensitivity-filter-level",
"position": 4
},
"doc": "The truth sensitivity level at which to start filtering",
"id": "#GATK4-ApplyVQSR.cwl/truth_sensitivity_filter_level"
},
{
"type": "File",
"inputBinding": {
"prefix": "-V",
"position": 1
},
"secondaryFiles": [
".idx"
],
"doc": "One or more VCF files containing variants This argument must be specified at least once.",
"id": "#GATK4-ApplyVQSR.cwl/variants"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.output_recalibrated_variants_filename)"
},
"secondaryFiles": [
".idx"
],
"id": "#GATK4-ApplyVQSR.cwl/output_recalibrated_variants"
}
],
"arguments": [
{
"valueFrom": "ApplyVQSR",
"position": 0
}
],
"id": "#GATK4-ApplyVQSR.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": "File",
"inputBinding": {
"prefix": "--DBSNP",
"position": 2
},
"secondaryFiles": [
".idx"
],
"doc": "Reference dbSNP file in dbSNP or VCF format. Required.",
"id": "#GATK4-CollectVariantCallingMetrics.cwl/dbsnp"
},
{
"type": "File",
"inputBinding": {
"prefix": "--INPUT",
"position": 1
},
"secondaryFiles": [
".idx"
],
"doc": "Input vcf file for analysis Required.",
"id": "#GATK4-CollectVariantCallingMetrics.cwl/input_vcf"
},
{
"type": "string",
"doc": "String of options to pass to JVM at runtime",
"inputBinding": {
"prefix": "--java-options",
"position": -1,
"shellQuote": true
},
"id": "#GATK4-CollectVariantCallingMetrics.cwl/java_opt"
},
{
"type": "string",
"inputBinding": {
"prefix": "--OUTPUT",
"position": 4
},
"doc": "Path (except for the file extension) of output metrics files to write.",
"id": "#GATK4-CollectVariantCallingMetrics.cwl/output_metrics_filename_prefix"
},
{
"type": [
"null",
"File"
],
"inputBinding": {
"prefix": "--SEQUENCE_DICTIONARY",
"position": 3
},
"doc": "If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here.",
"id": "#GATK4-CollectVariantCallingMetrics.cwl/sequence_dictionary"
},
{
"type": [
"null",
"File"
],
"inputBinding": {
"prefix": "--TARGET_INTERVALS",
"position": 6
},
"doc": "Target intervals to restrict analysis to.",
"id": "#GATK4-CollectVariantCallingMetrics.cwl/target_intervals"
},
{
"type": [
"null",
"int"
],
"inputBinding": {
"prefix": "--THREAD_COUNT",
"position": 5
},
"doc": "Number of threads to use (Undocumented in gatk CLI help)",
"id": "#GATK4-CollectVariantCallingMetrics.cwl/thread_count"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.output_metrics_filename_prefix + '.variant_calling_detail_metrics')"
},
"id": "#GATK4-CollectVariantCallingMetrics.cwl/output_detail_metrics"
},
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.output_metrics_filename_prefix + '.variant_calling_summary_metrics')"
},
"id": "#GATK4-CollectVariantCallingMetrics.cwl/output_summary_metrics"
}
],
"arguments": [
{
"valueFrom": "CollectVariantCallingMetrics",
"position": 0
}
],
"id": "#GATK4-CollectVariantCallingMetrics.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].",
"id": "#GATK4-GenotypeGVCFs.cwl/annotation_groups"
},
{
"type": [
"null",
"File"
],
"inputBinding": {
"prefix": "-D"
},
"secondaryFiles": [
".idx"
],
"doc": "dbSNP file. Default value: null",
"id": "#GATK4-GenotypeGVCFs.cwl/dbsnp"
},
{
"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-GenotypeGVCFs.cwl/interval_padding"
},
{
"type": [
"null",
{
"type": "array",
"items": "File",
"inputBinding": {
"prefix": "-L"
}
}
],
"doc": "One or more genomic intervals over which to operate",
"id": "#GATK4-GenotypeGVCFs.cwl/intervals"
},
{
"type": "string",
"doc": "String of options to pass to JVM at runtime",
"inputBinding": {
"prefix": "--java-options",
"position": -1,
"shellQuote": true
},
"id": "#GATK4-GenotypeGVCFs.cwl/java_opt"
},
{
"type": [
"null",
"boolean"
],
"inputBinding": {
"prefix": "--only_output_calls_starting_in_intervals"
},
"doc": "Restrict variant output to sites that start within provided intervals Default value: false.",
"id": "#GATK4-GenotypeGVCFs.cwl/only_output_calls_starting_in_intervals"
},
{
"type": "string",
"inputBinding": {
"prefix": "-O"
},
"doc": "File to which variants should be written Required.",
"id": "#GATK4-GenotypeGVCFs.cwl/output_vcf_filename"
},
{
"type": "File",
"inputBinding": {
"prefix": "-R"
},
"secondaryFiles": [
".amb",
".ann",
".bwt",
".pac",
".sa",
".fai",
"^.dict"
],
"doc": "Reference sequence file Required.",
"id": "#GATK4-GenotypeGVCFs.cwl/reference"
},
{
"type": [
"null",
"boolean"
],
"inputBinding": {
"prefix": "--use-new-qual-calculator"
},
"doc": "If provided, we will use the new AF model instead of the so-called exact model Default value: false.",
"id": "#GATK4-GenotypeGVCFs.cwl/use_new_qual_calculator"
},
{
"type": {
"type": "array",
"items": "File",
"inputBinding": {
"prefix": "-V"
}
},
"inputBinding": {
"position": 2
},
"doc": "One or more VCF files containing variants Required.",
"id": "#GATK4-GenotypeGVCFs.cwl/variants"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.output_vcf_filename)"
},
"secondaryFiles": [
".idx"
],
"id": "#GATK4-GenotypeGVCFs.cwl/output_vcf"
}
],
"arguments": [
{
"valueFrom": "GenotypeGVCFs",
"position": 0
}
],
"id": "#GATK4-GenotypeGVCFs.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": "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": {
"type": "array",
"items": "string",
"inputBinding": {
"prefix": "-an"
}
},
"inputBinding": {
"position": 6
},
"doc": "The names of the annotations which should used for calculations",
"id": "#GATK4-VariantRecalibrator.cwl/annotations"
},
{
"type": "string",
"doc": "String of options to pass to JVM at runtime",
"inputBinding": {
"prefix": "--java-options",
"position": -1,
"shellQuote": true
},
"id": "#GATK4-VariantRecalibrator.cwl/java_opt"
},
{
"type": [
"null",
"int"
],
"inputBinding": {
"prefix": "--max-gaussians",
"position": 8
},
"doc": "Max number of Gaussians for the positive model Default value: 8.",
"id": "#GATK4-VariantRecalibrator.cwl/max_gaussians"
},
{
"type": {
"type": "enum",
"symbols": [
"#GATK4-VariantRecalibrator.cwl/mode/SNP",
"#GATK4-VariantRecalibrator.cwl/mode/INDEL",
"#GATK4-VariantRecalibrator.cwl/mode/BOTH"
]
},
"inputBinding": {
"prefix": "-mode",
"position": 7
},
"doc": "Recalibration mode to employ Default value: SNP. Possible values: {SNP, INDEL, BOTH}",
"id": "#GATK4-VariantRecalibrator.cwl/mode"
},
{
"type": "string",
"inputBinding": {
"prefix": "-O",
"position": 2
},
"doc": "The output recal file used by ApplyRecalibration Required.",
"id": "#GATK4-VariantRecalibrator.cwl/output_recalibration_filename"
},
{
"type": "string",
"inputBinding": {
"prefix": "--tranches-file",
"position": 3
},
"doc": "The output tranches file used by ApplyRecalibration Required.",
"id": "#GATK4-VariantRecalibrator.cwl/output_tranches_filename"
},
{
"inputBinding": {
"position": 9
},
"type": {
"type": "array",
"items": {
"type": "record",
"name": "#GATK4-VariantRecalibrator.cwl/resources/resource",
"fields": [
{
"type": "File",
"name": "#GATK4-VariantRecalibrator.cwl/resources/resource/file"
},
{
"type": "boolean",
"name": "#GATK4-VariantRecalibrator.cwl/resources/resource/known"
},
{
"type": "string",
"name": "#GATK4-VariantRecalibrator.cwl/resources/resource/name"
},
{
"type": "int",
"name": "#GATK4-VariantRecalibrator.cwl/resources/resource/prior"
},
{
"type": "boolean",
"name": "#GATK4-VariantRecalibrator.cwl/resources/resource/training"
},
{
"type": "boolean",
"name": "#GATK4-VariantRecalibrator.cwl/resources/resource/truth"
}
]
},
"inputBinding": {
"prefix": "-resource",
"valueFrom": "${\n function makeResourceLine(resource) {\n return resource.name +\n ',known=' + (resource.known ? 'true' : 'false') +\n ',training=' + (resource.training ? 'true' : 'false') +\n ',truth=' + (resource.truth ? 'true' : 'false') +\n ',prior=' + resource.prior +\n ':' + resource.file.path;\n }\n return makeResourceLine(self);\n}\n"
}
},
"id": "#GATK4-VariantRecalibrator.cwl/resources"
},
{
"type": {
"type": "array",
"items": "string",
"inputBinding": {
"prefix": "-tranche"
}
},
"inputBinding": {
"position": 5
},
"id": "#GATK4-VariantRecalibrator.cwl/tranches"
},
{
"type": [
"null",
"boolean"
],
"inputBinding": {
"prefix": "--trust-all-polymorphic",
"position": 4
},
"doc": "Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation. Default value: false.",
"id": "#GATK4-VariantRecalibrator.cwl/trust_all_polymorphic"
},
{
"type": "File",
"inputBinding": {
"prefix": "-V",
"position": 1
},
"secondaryFiles": [
".idx"
],
"doc": "One or more VCF files containing variants Required.",
"id": "#GATK4-VariantRecalibrator.cwl/variants"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.output_recalibration_filename)"
},
"secondaryFiles": [
".idx"
],
"id": "#GATK4-VariantRecalibrator.cwl/output_recalibration"
},
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.output_tranches_filename)"
},
"id": "#GATK4-VariantRecalibrator.cwl/output_tranches"
}
],
"arguments": [
{
"valueFrom": "VariantRecalibrator",
"position": 0
}
],
"id": "#GATK4-VariantRecalibrator.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": "$(inputs.output_filename)"
},
"id": "#concat-gz-files.cwl/output"
}
],
"id": "#concat-gz-files.cwl"
},
{
"class": "ExpressionTool",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"inputs": [
{
"type": [
"null",
{
"type": "array",
"items": "File"
}
],
"id": "#extract-array-file.cwl/files"
},
{
"type": "int",
"id": "#extract-array-file.cwl/index"
}
],
"outputs": [
{
"type": "File",
"id": "#extract-array-file.cwl/extracted"
}
],
"expression": "${\n if(inputs.files) {\n return { \"extracted\" : inputs.files[inputs.index] };\n } else {\n return { \"extracted\" : null };\n }\n}\n",
"id": "#extract-array-file.cwl"
},
{
"class": "ExpressionTool",
"label": "Given a FASTQReadPairType returns a 2D array of the files contained within",
"requirements": [
{
"class": "InlineJavascriptRequirement"
},
{
"types": [
{
"$import": "#FASTQReadPairType.yml"
}
],
"class": "SchemaDefRequirement"
}
],
"inputs": [
{
"type": "string",
"id": "#extract-named-file-pair-details.cwl/library"
},
{
"type": "string",
"id": "#extract-named-file-pair-details.cwl/platform"
},
{
"type": "#FASTQReadPairType.yml/FASTQReadPairType",
"id": "#extract-named-file-pair-details.cwl/read_pair"
}
],
"outputs": [
{
"type": "string",
"id": "#extract-named-file-pair-details.cwl/read_group_header"
},
{
"type": "string",
"id": "#extract-named-file-pair-details.cwl/read_pair_name"
},
{
"type": {
"type": "array",
"items": {
"type": "array",
"items": "File"
}
},
"id": "#extract-named-file-pair-details.cwl/reads"
}
],
"expression": "${\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": "ExpressionTool",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"inputs": [
{
"type": "File",
"id": "#extract-secondary-file.cwl/file"
},
{
"type": "string",
"id": "#extract-secondary-file.cwl/pattern"
}
],
"outputs": [
{
"type": "File",
"id": "#extract-secondary-file.cwl/extracted"
}
],
"expression": "${\n var secondaryFiles = inputs.file.secondaryFiles;\n var pattern = inputs.pattern;\n var matches = secondaryFiles.filter(function(each) {\n return each.basename.match(pattern);\n });\n return { \"extracted\" : matches[0] };\n}\n",
"id": "#extract-secondary-file.cwl"
},
{
"class": "CommandLineTool",
"hints": [
{
"class": "DockerRequirement",
"dockerPull": "dukegcb/fastqc:0.11.4"
},
{
"class": "SoftwareRequirement",
"packages": [
{
"version": [
"0.11.4"
],
"package": "fastqc",
"https://schema.org/citation": "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
}
]
}
],
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"inputs": [
{
"type": "string",
"default": "fastq",
"inputBinding": {
"position": 3,
"prefix": "--format"
},
"id": "#fastqc.cwl/format"
},
{
"type": "File",
"inputBinding": {
"position": 4
},
"id": "#fastqc.cwl/input_fastq_file"
},
{
"type": "boolean",
"default": true,
"inputBinding": {
"prefix": "--noextract",
"position": 2
},
"id": "#fastqc.cwl/noextract"
},
{
"type": "int",
"default": 1,
"doc": "The number of threads to use. The fastqc wrapper script requests 250MB of memory per thread, so keep this in line with any CWL ResourceRequirement",
"inputBinding": {
"position": 5,
"prefix": "--threads"
},
"id": "#fastqc.cwl/threads"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "*_fastqc.zip"
},
"id": "#fastqc.cwl/output_qc_report"
}
],
"baseCommand": "fastqc",
"arguments": [
{
"valueFrom": "$('/tmp')",
"prefix": "--dir",
"position": 5
},
{
"valueFrom": "$(runtime.outdir)",
"prefix": "-o",
"position": 5
}
],
"id": "#fastqc.cwl"
},
{
"class": "ExpressionTool",
"label": "Moves an array of File pairs into a named directory",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"inputs": [
{
"type": {
"type": "array",
"items": {
"type": "array",
"items": "File"
}
},
"id": "#file-pairs-to-directory.cwl/file_pairs"
},
{
"type": "string",
"id": "#file-pairs-to-directory.cwl/name"
}
],
"outputs": [
{
"type": "Directory",
"id": "#file-pairs-to-directory.cwl/outdir"
}
],
"expression": "${\n var files = inputs.file_pairs.reduce(function(a,b) {\n return a.concat(b);\n }, []);\n\n var result = {\n outdir: {\n class: 'Directory',\n basename: inputs.name,\n listing: files\n }\n };\n\n return result;\n}\n",
"id": "#file-pairs-to-directory.cwl"
},
{
"class": "ExpressionTool",
"label": "Moves an array of Files into a named directory",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"inputs": [
{
"type": {
"type": "array",
"items": "File"
},
"id": "#files-to-directory.cwl/files"
},
{
"type": "string",
"id": "#files-to-directory.cwl/name"
}
],
"outputs": [
{
"type": "Directory",
"id": "#files-to-directory.cwl/outdir"
}
],
"expression": "${\n var result = {\n outdir: {\n class: 'Directory',\n basename: inputs.name,\n listing: inputs.files\n }\n };\n\n return result;\n}\n",
"id": "#files-to-directory.cwl"
},
{
"class": "ExpressionTool",
"label": "Generates a set of file names for joint steps based on an input name",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"inputs": [
{
"type": "string",
"id": "#generate-joint-filenames.cwl/name"
}
],
"outputs": [
{
"type": "string",
"id": "#generate-joint-filenames.cwl/combined_recalibrated_variants_filename"
},
{
"type": "string",
"id": "#generate-joint-filenames.cwl/indels_recalibrated_variants_filename"
},
{
"type": "string",
"id": "#generate-joint-filenames.cwl/indels_recalibration_filename"
},
{
"type": "string",
"id": "#generate-joint-filenames.cwl/indels_tranches_filename"
},
{
"type": "string",
"id": "#generate-joint-filenames.cwl/raw_variants_filename"
},
{
"type": "string",
"id": "#generate-joint-filenames.cwl/snps_recalibrated_variants_filename"
},
{
"type": "string",
"id": "#generate-joint-filenames.cwl/snps_recalibration_filename"
},
{
"type": "string",
"id": "#generate-joint-filenames.cwl/snps_tranches_filename"
}
],
"expression": "${\n function makeFilename(base, suffix, extension) {\n return base + '-' + suffix + '.' + extension;\n }\n var base = inputs.name\n\n return {\n raw_variants_filename: makeFilename(base, 'raw_variants', 'g.vcf'),\n snps_recalibration_filename: makeFilename(base, 'snps_recal', 'out'),\n snps_tranches_filename: makeFilename(base, 'snps_tranches', 'out'),\n snps_recalibrated_variants_filename: makeFilename(base, 'snps_recal_variants', 'vcf'),\n indels_recalibration_filename: makeFilename(base, 'indels_recal', 'out'),\n indels_tranches_filename: makeFilename(base, 'indels_tranches', 'out'),\n indels_recalibrated_variants_filename: makeFilename(base, 'indels_recal_variants', 'vcf'),\n combined_recalibrated_variants_filename: makeFilename(base, 'indels_snps_recal_variants', 'vcf')\n };\n}\n",
"id": "#generate-joint-filenames.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": "${\n function makeFilename(base, suffix, extension) {\n return base + '-' + suffix + '.' + extension;\n }\n var base = inputs.sample_name\n\n return {\n combined_reads_output_filenames: [\n makeFilename(base, 'R1', 'fastq.gz'),\n makeFilename(base, 'R2', 'fastq.gz'),\n ],\n mapped_reads_output_filename: makeFilename(base, 'mapped', 'bam'),\n sorted_reads_output_filename: makeFilename(base, 'sorted', 'bam'),\n dedup_reads_output_filename: makeFilename(base, 'dedup', 'bam'),\n dedup_metrics_output_filename: makeFilename(base, 'dedup-metrics', 'out'),\n recal_reads_output_filename: makeFilename(base, 'recal', 'bam'),\n recal_table_output_filename: makeFilename(base, 'recal', 'table'),\n raw_variants_output_filename: makeFilename(base, 'raw_variants', 'g.vcf'),\n haplotypes_bam_output_filename: makeFilename(base, 'haplotypes', 'bam'),\n hs_metrics_output_filename: makeFilename(base, 'hs', 'txt'),\n fixedtag_reads_output_filename: makeFilename(base, 'fixed_tags', 'bam')\n };\n}\n",
"id": "#generate-sample-filenames.cwl"
},
{
"class": "ExpressionTool",
"label": "Given an ExomeseqStudyType returns an array of the annotations to use.",
"doc": "The InbreedingCoeff is a population level statistic that requires at least 10 samples in order to be computed. For projects with fewer samples, or that includes many closely related samples (such as a family) please omit this annotation from the command line. From https://software.broadinstitute.org/gatk/documentation/article?id=1259\n",
"requirements": [
{
"class": "InlineJavascriptRequirement"
},
{
"types": [
{
"$import": "#ExomeseqStudyType.yml"
}
],
"class": "SchemaDefRequirement"
}
],
"inputs": [
{
"type": {
"type": "array",
"items": "string"
},
"id": "#generate-variant-recalibration-annotation-set.cwl/base_annotations"
},
{
"type": "#ExomeseqStudyType.yml/ExomeseqStudyType",
"id": "#generate-variant-recalibration-annotation-set.cwl/study_type"
}
],
"outputs": [
{
"type": {
"type": "array",
"items": "string"
},
"id": "#generate-variant-recalibration-annotation-set.cwl/annotations"
}
],
"expression": "${\n var annotations = inputs.base_annotations;\n var inputStudyType = inputs.study_type;\n if(inputStudyType === \"Large Population\") {\n annotations.push(\"InbreedingCoeff\");\n }\n return {\"annotations\": annotations };\n}\n",
"id": "#generate-variant-recalibration-annotation-set.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": {
"glob": "*_trimming_report.txt"
},
"id": "#trim_galore.cwl/trim_reports"
},
{
"type": {
"type": "array",
"items": "File"
},
"outputBinding": {
"glob": "*_val_*.fq*"
},
"id": "#trim_galore.cwl/trimmed_reads"
}
],
"baseCommand": "trim_galore",
"arguments": [
{
"valueFrom": "$(runtime.outdir)",
"prefix": "-o",
"position": 2
}
],
"id": "#trim_galore.cwl"
},
{
"class": "Workflow",
"label": "WES GATK4",
"doc": "Whole Exome Sequence analysis GATK4 Preprocessing\n",
"requirements": [
{
"class": "ScatterFeatureRequirement"
},
{
"class": "SubworkflowFeatureRequirement"
},
{
"class": "SchemaDefRequirement",
"types": [
{
"$import": "#ExomeseqStudyType.yml"
},
{
"$import": "#FASTQReadPairType.yml"
}
]
}
],
"inputs": [
{
"type": [
"null",
{
"type": "array",
"items": "File"
}
],
"id": "#main/bait_intervals"
},
{
"type": "File",
"secondaryFiles": [
".idx"
],
"id": "#main/indel_resource_mills"
},
{
"type": [
"null",
"int"
],
"id": "#main/interval_padding"
},
{
"type": {
"type": "array",
"items": "File"
},
"secondaryFiles": [
".idx"
],
"id": "#main/known_sites"
},
{
"type": "string",
"id": "#main/library"
},
{
"type": "string",
"id": "#main/platform"
},
{
"type": {
"type": "array",
"items": "#FASTQReadPairType.yml/FASTQReadPairType"
},
"id": "#main/read_pairs"
},
{
"type": "File",
"secondaryFiles": [
".amb",
".ann",
".bwt",
".pac",
".sa",
".fai",
"^.dict"
],
"id": "#main/reference_genome"
},
{
"type": "File",
"secondaryFiles": [
".idx"
],
"id": "#main/resource_dbsnp"
},
{
"type": "File",
"secondaryFiles": [
".idx"
],
"id": "#main/snp_resource_1kg"
},
{
"type": "File",
"secondaryFiles": [
".idx"
],
"id": "#main/snp_resource_hapmap"
},
{
"type": "File",
"secondaryFiles": [
".idx"
],
"id": "#main/snp_resource_omni"
},
{
"type": "#ExomeseqStudyType.yml/ExomeseqStudyType",
"id": "#main/study_type"
},
{
"type": [
"null",
{
"type": "array",
"items": "File"
}
],
"id": "#main/target_intervals"
},
{
"type": "int",
"id": "#main/threads"
}
],
"outputs": [
{
"type": "Directory",
"outputSource": "#main/organize_directories/bams_markduplicates_dir",
"doc": "BAM and bai files from markduplicates",
"id": "#main/bams_markduplicates_dir"
},
{
"type": "Directory",
"outputSource": "#main/organize_directories/bams_recalibrated_dir",
"doc": "BAM files containing recalibrated reads",
"id": "#main/bams_recalibrated_dir"
},
{
"type": "Directory",
"outputSource": "#main/organize_directories/fastqc_reports_dir",
"id": "#main/fastqc_reports_dir"
},
{
"type": "File",
"outputSource": "#main/variant_discovery/variant_recalibration_combined_vcf",
"doc": "The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value",
"id": "#main/filtered_recalibrated_variants"
},
{
"type": "File",
"outputSource": "#main/variant_discovery/joint_raw_variants",
"doc": "GVCF file from joint genotyping calling",
"id": "#main/joint_raw_variants"
},
{
"type": "Directory",
"outputSource": "#main/organize_directories/raw_variants_dir",
"id": "#main/raw_variants_dir"
},
{
"type": "Directory",
"outputSource": "#main/organize_directories/trim_reports_dir",
"id": "#main/trim_reports_dir"
},
{
"type": "File",
"outputSource": "#main/variant_discovery/detail_metrics",
"id": "#main/variant_calling_detail_metrics"
},
{
"type": "File",
"outputSource": "#main/variant_discovery/summary_metrics",
"id": "#main/variant_calling_summary_metrics"
}
],
"steps": [
{
"run": "#exomeseq-gatk4-03-organizedirectories.cwl",
"in": [
{
"source": "#main/preprocessing/markduplicates_bam",
"id": "#main/organize_directories/bams_markduplicates"
},
{
"source": "#main/preprocessing/recalibrated_reads",
"id": "#main/organize_directories/bams_recalibrated"
},
{
"source": "#main/preprocessing/fastqc_reports",
"id": "#main/organize_directories/fastqc_reports"
},
{
"source": "#main/preprocessing/raw_variants",
"id": "#main/organize_directories/raw_variants"
},
{
"source": "#main/preprocessing/trim_reports",
"id": "#main/organize_directories/trim_reports"
}
],
"out": [
"#main/organize_directories/fastqc_reports_dir",
"#main/organize_directories/trim_reports_dir",
"#main/organize_directories/bams_markduplicates_dir",
"#main/organize_directories/raw_variants_dir",
"#main/organize_directories/bams_recalibrated_dir"
],
"id": "#main/organize_directories"
},
{
"run": "#exomeseq-00-prepare-reference-data.cwl",
"in": [
{
"source": "#main/bait_intervals",
"id": "#main/prepare_reference_data/bait_intervals"
},
{
"source": "#main/reference_genome",
"id": "#main/prepare_reference_data/reference_genome"
},
{
"source": "#main/target_intervals",
"id": "#main/prepare_reference_data/target_intervals"
}
],
"out": [
"#main/prepare_reference_data/target_interval_list",
"#main/prepare_reference_data/bait_interval_list"
],
"id": "#main/prepare_reference_data"
},
{
"run": "#exomeseq-gatk4-01-preprocessing.cwl",
"scatter": "#main/preprocessing/read_pair",
"in": [
{
"source": "#main/prepare_reference_data/bait_interval_list",
"id": "#main/preprocessing/bait_interval_list"
},
{
"source": "#main/interval_padding",
"id": "#main/preprocessing/interval_padding"
},
{
"source": "#main/target_intervals",
"id": "#main/preprocessing/intervals"
},
{
"source": "#main/known_sites",
"id": "#main/preprocessing/known_sites"
},
{
"source": "#main/library",
"id": "#main/preprocessing/library"
},
{
"source": "#main/platform",
"id": "#main/preprocessing/platform"
},
{
"source": "#main/read_pairs",
"id": "#main/preprocessing/read_pair"
},
{
"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"
},
{
"run": "#exomeseq-gatk4-02-variantdiscovery.cwl",
"in": [
{
"source": "#main/indel_resource_mills",
"id": "#main/variant_discovery/indel_resource_mills"
},
{
"source": "#main/interval_padding",
"id": "#main/variant_discovery/interval_padding"
},
{
"source": "#main/target_intervals",
"id": "#main/variant_discovery/intervals"
},
{
"source": "#main/library",
"id": "#main/variant_discovery/name"
},
{
"source": "#main/preprocessing/raw_variants",
"id": "#main/variant_discovery/raw_variants"
},
{
"source": "#main/reference_genome",
"id": "#main/variant_discovery/reference_genome"
},
{
"source": "#main/resource_dbsnp",
"id": "#main/variant_discovery/resource_dbsnp"
},
{
"source": "#main/snp_resource_1kg",
"id": "#main/variant_discovery/snp_resource_1kg"
},
{
"source": "#main/snp_resource_hapmap",
"id": "#main/variant_discovery/snp_resource_hapmap"
},
{
"source": "#main/snp_resource_omni",
"id": "#main/variant_discovery/snp_resource_omni"
},
{
"source": "#main/study_type",
"id": "#main/variant_discovery/study_type"
}
],
"out": [
"#main/variant_discovery/joint_raw_variants",
"#main/variant_discovery/variant_recalibration_snps_tranches",
"#main/variant_discovery/variant_recalibration_snps_recalibration",
"#main/variant_discovery/variant_recalibration_combined_vcf",
"#main/variant_discovery/variant_recalibration_indels_tranches",
"#main/variant_discovery/variant_recalibration_snps_indels_recalibration",
"#main/variant_discovery/variant_recalibration_indels_vcf",
"#main/variant_discovery/detail_metrics",
"#main/variant_discovery/summary_metrics"
],
"id": "#main/variant_discovery"
}
],
"id": "#main"
}
],
"cwlVersion": "v1.0",
"$schemas": [
"https://schema.org/docs/schema_org_rdfa.html"
]
}
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