@prefix LoadListingRequirement: . @prefix NetworkAccess: . @prefix rdf: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix cwl: . @prefix sld: . @prefix ResourceRequirement: . @prefix CommandOutputBinding: . @prefix ns1: . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".gc_bias.detail_metrics\")" ] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".pre_adapter_detail_metrics\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/picard_metrics_sqlite" "--metric_name" "CollectMultipleMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/picard_metrics_sqlite:e71798322233d02d67db0158aeeef27990d2d400aadfc92c3687ba85555b0cf8" ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".base_distribution_by_cycle.pdf\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".insert_size_histogram.pdf\")" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . sld:type xsd:long . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:inputBinding [ CommandLineBinding:prefix "--alignment_summary_metrics" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".pre_adapter_summary_metrics\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".idxstats\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--quality_distribution_metrics" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--insert_size_metrics" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".alignment_summary_metrics\")" ] ; sld:type cwl:File . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.basename + \".oxometrics\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--quality_yield_metrics" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--pre_adapter_detail_metrics" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--gc_bias_summary_metrics" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools_metrics_sqlite" "--metric_name" "stats" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/samtools_metrics_sqlite:f64466282ce61dfc9251e7c32c5130928abf0a68c1f8e00b47d9709c5b3e3321" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_CollectWgsMetrics.log\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".flagstat\")" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".bait_bias_detail_metrics\")" ] ; sld:type cwl:File . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.INPUT.basename + \".oxometrics\")" ] ) ; cwl:baseCommand ( "java" "-jar" "/usr/local/bin/picard.jar" "CollectOxoGMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 10000 ; ResourceRequirement:ramMin 10000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/picard:092d034713aff237cf07ef28c22a46a113d1a59dc7ec6d71beb72295044a46f8" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".quality_distribution.pdf\")" ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools" "stats" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/samtools:147bd4cc606a63c7435907d97fea6e94e9ea9ed58c18f390cab8bc40b1992df7" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 5000 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.INPUT.nameroot + \".stats\")" . cwl:source . cwl:source , , , , , . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.INPUT.nameroot + \".metrics\")" ] ) ; cwl:baseCommand ( "java" "-jar" "/usr/local/bin/picard.jar" "CollectWgsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 10000 ; ResourceRequirement:ramMin 10000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/picard:092d034713aff237cf07ef28c22a46a113d1a59dc7ec6d71beb72295044a46f8" ] . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , ; cwl:out , ; cwl:run . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--quality_by_cycle_metrics" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".gc_bias.summary_metrics\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".metrics\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_CollectOxoGMetrics.log\")" ] ; sld:type cwl:File . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "PROGRAM=CollectAlignmentSummaryMetrics" ] [ cwl:valueFrom "PROGRAM=CollectBaseDistributionByCycle" ] [ cwl:valueFrom "PROGRAM=CollectGcBiasMetrics" ] [ cwl:valueFrom "PROGRAM=CollectInsertSizeMetrics" ] [ cwl:valueFrom "PROGRAM=CollectQualityYieldMetrics" ] [ cwl:valueFrom "PROGRAM=CollectSequencingArtifactMetrics" ] [ cwl:valueFrom "PROGRAM=MeanQualityByCycle" ] [ cwl:valueFrom "PROGRAM=QualityScoreDistribution" ] [ CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.INPUT.nameroot)" ] ) ; cwl:baseCommand ( "java" "-jar" "/usr/local/bin/picard.jar" "CollectMultipleMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs , , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 10000 ; ResourceRequirement:ramMin 10000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/picard:092d034713aff237cf07ef28c22a46a113d1a59dc7ec6d71beb72295044a46f8" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string . cwl:default "true" ; cwl:inputBinding [ CommandLineBinding:prefix "USE_OQ=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string . cwl:in , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/picard_metrics_sqlite" "--metric_name" "CollectWgsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/picard_metrics_sqlite:e71798322233d02d67db0158aeeef27990d2d400aadfc92c3687ba85555b0cf8" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "--base_distribution_by_cycle_metrics" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_CollectMultipleMetrics.log\")" ] ; sld:type cwl:File . cwl:source . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "DB_SNP=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".quality_yield_metrics\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--pre_adapter_summary_metrics" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".base_distribution_by_cycle_metrics\")" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools_metrics_sqlite" "--metric_name" "flagstat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/samtools_metrics_sqlite:f64466282ce61dfc9251e7c32c5130928abf0a68c1f8e00b47d9709c5b3e3321" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".gc_bias.pdf\")" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:format ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:source . cwl:default "LIBRARY" , "READ_GROUP" , "SAMPLE" , "ALL_READS" ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ; CommandLineBinding:separate false ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".stats\")" ] ; sld:type cwl:File . cwl:format ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_samtools_stats.log\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".quality_by_cycle.pdf\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".quality_distribution_metrics\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "TMP_DIR=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--bait_bias_summary_metrics" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "TMP_DIR=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , , , , , , , , , , , , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".bait_bias_summary_metrics\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_samtools_flagstat.log\")" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools_metrics_sqlite" "--metric_name" "idxstats" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/samtools_metrics_sqlite:f64466282ce61dfc9251e7c32c5130928abf0a68c1f8e00b47d9709c5b3e3321" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".quality_by_cycle_metrics\")" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "DB_SNP=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".insert_size_metrics\")" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/merge_sqlite" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/merge_sqlite:1b3a6f55be8579ecfb4c9c0513c3b710717a8f4cd8e79c88ee8c0f28f604faa3" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n} \n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(2 * (req_space / 1048576));\n} \n" ; ResourceRequirement:tmpdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(2 * (req_space / 1048576));\n} \n" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:in , , ; cwl:out , , , , , , , , , , , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools" "flagstat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 5000 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/samtools:147bd4cc606a63c7435907d97fea6e94e9ea9ed58c18f390cab8bc40b1992df7" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.INPUT.nameroot + \".flagstat\")" . cwl:inputBinding [ CommandLineBinding:prefix "--bait_bias_detail_metrics" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_samtools_idxstats.log\")" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.basename)" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/picard_metrics_sqlite" "--metric_name" "CollectOxoGMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/picard_metrics_sqlite:e71798322233d02d67db0158aeeef27990d2d400aadfc92c3687ba85555b0cf8" ] . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:format ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:format ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--gc_bias_detail_metrics" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools" "idxstats" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/ncigdc/samtools:147bd4cc606a63c7435907d97fea6e94e9ea9ed58c18f390cab8bc40b1992df7" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 5000 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:stdout "$(inputs.INPUT.nameroot + \".idxstats\")" . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; sld:type xsd:string .