@prefix LoadListingRequirement: . @prefix SchemaDefRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix ScatterMethod: . @prefix cwl: . @prefix ResourceRequirement: . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.interval_list.nameroot).expanded.interval_list" ] ; sld:type cwl:File . cwl:default "indel" . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--tumor-sample-name" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "mutect.filtered.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 50 ; sld:type xsd:int . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; sld:type sld:null , xsd:boolean . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "out" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "all_SI" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--referenceFasta=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self)_full" . cwl:source ; cwl:valueFrom "base-$(self.label)" . cwl:source . cwl:source . cwl:default "merged" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "per_chromosome_pindel.out" ] ; sld:type cwl:File . sld:type xsd:string . sld:type xsd:string . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; sld:type sld:null , xsd:int . cwl:source . cwl:default 400 ; sld:type xsd:int . cwl:in ; cwl:out ; cwl:run . rdfs:comment "select only a certain type of variants" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] . sld:type xsd:float , sld:null . cwl:in ; cwl:out ; cwl:run . sld:type xsd:float , sld:null . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--species" ] ; sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "Mark duplicates and Sort" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 4 ; cwl:valueFrom "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 4 ; cwl:valueFrom "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ) ; cwl:baseCommand ( "/bin/bash" "markduplicates_helper.sh" ) ; cwl:baseCommand ( "/bin/bash" "markduplicates_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] . sld:type xsd:int , sld:null . cwl:source . sld:type cwl:File . cwl:source . sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:string . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "all_INV" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; rdfs:label "bgzip VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:stdout "$(inputs.file.basename).gz" . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . sld:type xsd:string . cwl:default true . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position -1 ] ; cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type cwl:File . a cwl:Workflow ; rdfs:label "Per-region pindel" ; 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:MultipleInputFeatureRequirement ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Picard MergeVcfs" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 40000 ] . cwl:source . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:source . sld:type cwl:File , sld:null . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; rdfs:label "add GT tags" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "add_strelka_gt.pl" "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/perl\n\nuse strict;\nuse warnings;\n\nuse feature qw(say);\n\ndie(\"wrong number of arguments\") unless scalar(@ARGV) == 2;\nmy ($strelka_vcf, $outdir) = @ARGV;\n\nopen(my $strelka_vcf_fh, '-|', '/bin/gunzip', '-c', $strelka_vcf) \n or die(\"couldn't open $strelka_vcf to read\");\nopen(my $add_gt_fh, \">\", \"$outdir/add_gt.vcf\") \n or die(\"couldn't open add_gt.vcf for write\");\n\nwhile (<$strelka_vcf_fh>) {\n chomp;\n if (/^##/) {\n say $add_gt_fh $_;\n }\n elsif (/^#/) { #COLUMN HEADER\n say $add_gt_fh '##FORMAT=';\n say $add_gt_fh $_;\n }\n else {\n my @columns = split /\\t/, $_;\n my ($ref, $alt, $info) = map{$columns[$_]}(3, 4, 7);\n my @alts = split /,/, $alt;\n\n my ($n_gt, $t_gt);\n\n if (length($ref) == 1 and length($alts[0]) == 1) {\n my ($n_gt_info, $n_gt_str, $t_gt_str) = $info =~ /NT=(\\S+?);QSS.*SGT=(\\S+?)\\->(\\S+?);/;\n unshift @alts, $ref;\n\n my %ids;\n my $id = 0;\n\n for my $base (@alts) {\n $ids{$base} = $id;\n $id++;\n }\n\n $n_gt = $n_gt_info eq 'ref' ? '0/0' : parse_gt($n_gt_str, \\%ids);\n $t_gt = parse_gt($t_gt_str, \\%ids);\n }\n else {#INDEL\n my ($n_gt_info, $t_gt_info) = $info =~ /;NT=(\\S+?);.*SGT.*\\->(\\S+?);/;\n\n my %gt_info = (\n ref => '0/0',\n het => '0/1',\n hom => '1/1',\n conflict => './.',\n );\n\n $n_gt = $gt_info{$n_gt_info};\n $t_gt = $gt_info{$t_gt_info};\n }\n\n $columns[8] = 'GT:'.$columns[8];\n $columns[9] = $n_gt . ':' . $columns[9];\n $columns[10] = $t_gt . ':' . $columns[10];\n\n my $new_str = join \"\\t\", @columns;\n say $add_gt_fh $new_str;\n }\n}\n\nclose($strelka_vcf_fh);\nclose($add_gt_fh);\n\n\nsub parse_gt {\n my ($gt_str, $ids) = @_;\n my @gt_ids = map{$ids->{$_}}(split //, $gt_str);\n return join '/', sort @gt_ids;\n}\n\n#SNV example\n#1 10231 . C A . QSS_ref NT=ref;QSS=1;QSS_NT=1;SGT=AC->AC;SOMATIC;TQSS=2;TQSS_NT=2 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 32:4:8:0:0,3:28,60:0,0:0,1 84:6:69:0:7,21:71,192:0,0:0,1\n#INDEL example\n##1 965051 . ATGTGTG A . QSI_ref IC=5;IHP=2;NT=ref;QSI=1;QSI_NT=1;RC=8;RU=TG;SGT=het->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50 8:8:6,6:0,0:2,4:10.3:0.00:0.00 18:18:8,8:5,6:5,8:21:0.25:0.00\n" ; cwl:entryname "add_strelka_gt.pl" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1" ; cwl:default 1 ; sld:type xsd:float . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:valueFrom "varscan" . cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--minimum_depth" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:float , sld:null . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "all_LI" ] ; sld:type cwl:File . rdfs:comment "Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1" ; cwl:default 1 ; sld:type xsd:float . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:Workflow ; rdfs:label "process VCF workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs . sld:type cwl:File . cwl:source . cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--everything" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--variant:varscan" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self).bam" . cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_snv.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_snv.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; sld:type cwl:File . cwl:default "AD" , "GT" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "add_gt.vcf" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:valueFrom "mutect" . cwl:in , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_indel.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_indel.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default true . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:in , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "use the binomial/llr somatic filter to weed out low confidence variants" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--overwrite" [ cwl:valueFrom "$(runtime.outdir)/somatic_llr_filtered.vcf" ] ) ; cwl:baseCommand ( "/opt/conda/bin/python3" "/usr/bin/somatic_llr_filter.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/somatic-llr-filter:v0.4.3" ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "Varscan 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:source . cwl:in , , , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type cwl:Directory , xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:default "AD" , "AF" , "DP" , "GT" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:valueFrom "ALL_READS" . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string . cwl:source . sld:type xsd:boolean . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "combined.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "filter" ] ; sld:type xsd:boolean . sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default 8 ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . sld:type xsd:boolean . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 somatic" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "varscan_helper.sh" ) ; 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 "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 2 ; ResourceRequirement:ramMin 12000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\n\nset -o errexit\nset -o nounset\n\nif [ $# -lt 7 ]\nthen\n echo \"Usage: $0 [TUMOR_BAM] [NORMAL_BAM] [REFERENCE] [STRAND_FILTER] [MIN_COVERAGE] [MIN_VAR_FREQ] [P_VALUE] [roi_bed?]\"\n exit 1\nfi\n\nTUMOR_BAM=\"$1\"\nNORMAL_BAM=\"$2\"\nREFERENCE=\"$3\"\nSTRAND_FILTER=\"$4\"\nMIN_COVERAGE=\"$5\"\nMIN_VAR_FREQ=\"$6\"\nP_VALUE=\"$7\"\nOUTPUT=\"${HOME}/output\"\n\nif [ -z ${8+x} ]\nthen\n #run without ROI\n java -jar /opt/varscan/VarScan.jar somatic \\\n <(/opt/samtools/bin/samtools mpileup --no-baq -f \"$REFERENCE\" \"$NORMAL_BAM\" \"$TUMOR_BAM\") \\\n $OUTPUT \\\n --strand-filter $STRAND_FILTER \\\n --min-coverage $MIN_COVERAGE \\\n --min-var-freq $MIN_VAR_FREQ \\\n --p-value $P_VALUE \\\n --mpileup 1 \\\n --output-vcf\nelse\n ROI_BED=\"$8\"\n java -jar /opt/varscan/VarScan.jar somatic \\\n <(/opt/samtools/bin/samtools mpileup --no-baq -l \"$ROI_BED\" -f \"$REFERENCE\" \"$NORMAL_BAM\" \"$TUMOR_BAM\") \\\n $OUTPUT \\\n --strand-filter $STRAND_FILTER \\\n --min-coverage $MIN_COVERAGE \\\n --min-var-freq $MIN_VAR_FREQ \\\n --p-value $P_VALUE \\\n --mpileup 1 \\\n --output-vcf\nfi\n" ; cwl:entryname "varscan_helper.sh" ] ] . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Normalize variants" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx8g" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx8g" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx8g" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx8g" "LeftAlignAndTrimVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] . cwl:outputBinding [ CommandOutputBinding:glob "somatic_llr_filtered.vcf" ] ; sld:type cwl:File . sld:type xsd:string . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:source . cwl:in , ; cwl:out ; cwl:run . a cwl:Workflow ; rdfs:label "fp_filter workflow" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:outputSource ; sld:type cwl:File . cwl:valueFrom "strelka" . rdfs:comment "target_intervals is an interval_list corresponding to the targets for the capture reagent.\nBed files with this information can be converted to interval_lists with Picard BedToIntervalList.\nIn general for a WES exome reagent bait_intervals and target_intervals are the same.\n" ; rdfs:label "target_intervals: interval_list file of targets used in the sequencing experiment" ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:int . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--fasta" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:default 1.5e-01 ; sld:type xsd:float . sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . a cwl:Workflow ; rdfs:label "Add snv and indel bam-readcount files to a vcf" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:default "AD" , "GT" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:int . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:default "TUMOR" . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-c" ] ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect alignment summary metrics" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "OUTPUT=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ) ; cwl:arguments ( "OUTPUT=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:source . cwl:source . cwl:default "DNA" . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; sld:type xsd:boolean . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "include genotypes from this sample" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--assembly" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:default "ALL_READS" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant:mutect" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . sld:type cwl:File . cwl:default 1e-01 ; sld:type xsd:float , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . a cwl:CommandLineTool ; rdfs:label "sort BAM by name" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-t" [ cwl:valueFrom "$(runtime.cores)" ] "-m" "22G" "-n" "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:arguments ( "-t" [ cwl:valueFrom "$(runtime.cores)" ] "-m" "22G" "-n" "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 26000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 26000 ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "filter vcf for variants with high percentage of mapq0 reads" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/bin/bash" "/usr/bin/mapq0_vcf_filter.sh" [ cwl:valueFrom "$(runtime.outdir)/mapq_filtered.vcf.gz" ] ) ; 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:ramMin 8000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mapq0-filter:v0.3.1" ] . cwl:inputBinding [ CommandLineBinding:prefix "--normal-sample-name" ] ; sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "annotated_filtered.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:source . cwl:source . rdfs:label "Force report the overlapping coordinates of custom feature instead of based on the exact coordinates" ; sld:type xsd:boolean . cwl:source . sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default 400 ; sld:type xsd:int . rdfs:label "Use this annotation for gnomad filtering?" ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.interval_list" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.interval_list" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default false . cwl:source . cwl:default "TUMOR" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "all_D" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Sample name to replace the other" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:in , , , , , , , , ; cwl:out , , , ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "depth_filtered.vcf" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "pindel.noend.vcf.gz" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "vcf merge" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:in , ; cwl:out , , , , , ; cwl:run . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "pindel somatic filter v1" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "/usr/bin/write_pindel_filter_config.pl" "$(inputs.pindel_output_summary.path)" "$(inputs.reference)" "$(runtime.outdir)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/perl" "/usr/bin/somatic_indelfilter.pl" "filter.config" ) ; 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:ramMin 16000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "align with bwa_mem and tag" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 4 ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( [ CommandLineBinding:position 4 ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/bin/bash" "/usr/bin/alignment_helper.sh" ) ; cwl:baseCommand ( "/bin/bash" "/usr/bin/alignment_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:stdout "refAlign.bam" . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1" ; cwl:default 0 ; sld:type xsd:float . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name).merged.bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name).merged.bam" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 processSomatic" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic" ) ; cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs , , , , , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; sld:type cwl:File . cwl:valueFrom "somatic_hc_indels" . cwl:source . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:in , , , , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; rdfs:label "run vt decompose" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:in , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . rdfs:comment "scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs" ; sld:type xsd:int . sld:type xsd:int , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out , , , , , , , , , ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "output.snp.vcf" ] ; sld:type cwl:File . cwl:default "NORMAL" . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 4.1.8.1)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "VariantsToTable" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "Unaligned to aligned BAM" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "pindel v0.2.5b8" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "pindel_helper.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/perl\n\nuse strict;\nuse warnings;\n\nuse IO::File;\n\nunless (@ARGV > 5) {\n die \"Usage: $0 normal.bam tumor.bam insert_size normal_sample_name tumor_sample_name \";\n}\n\nmy ($normal_bam, $tumor_bam, $insert_size, $normal_name, $tumor_name, @args) = @ARGV;\n\nmy $fh = IO::File->new(\"> pindel.config\");\n\n$fh->say(join(\"\\t\", $normal_bam, $insert_size, $normal_name));\n$fh->say(join(\"\\t\", $tumor_bam, $insert_size, $tumor_name));\n$fh->close;\n\nexit system(qw(/usr/bin/pindel -i pindel.config -w 30 -T 4 -o all), @args);\n" ; cwl:entryname "pindel_helper.pl" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.4.2" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 16000 ; ResourceRequirement:tmpdirMin 100000 ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:default 1e-01 ; sld:type xsd:float , sld:null . cwl:source . cwl:default false . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . a cwl:Workflow ; rdfs:label "exome alignment with qc, no bqsr, no verify_bam_id" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . rdfs:comment "Sample name to be replaced" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "roi_intervals is a list of regions (in interval_list format) within which to call somatic variants" ; rdfs:label "roi_intervals: regions of interest in which variants will be called" ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.interval.bed" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$((self.secondaryFiles !== undefined) ? self.secondaryFiles.find(function(x) { return x.nameext === \".dict\" }) : self.replace(/.fa$/,\".dict\") )" . cwl:outputSource ; sld:type cwl:File . cwl:default "DNA" . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:default "merged" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/perl" "intervals_to_bed.pl" ) ; 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 "ubuntu:bionic" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "use feature qw(say);\n\nfor my $line (<>) {\n chomp $line;\n\n next if substr($line,0,1) eq '@'; #skip header lines\n\n my ($chrom, $start, $stop) = split(/\\t/, $line);\n say(join(\"\\t\", $chrom, $start-1, $stop));\n}\n" ; cwl:entryname "intervals_to_bed.pl" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "interval_list.bed" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ] ) ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "split_interval_list_helper.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "split_interval_list_helper.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "use File::Copy;\n\nmy $retval = system('/usr/bin/java', '-jar', '/usr/picard/picard.jar', 'IntervalListTools', @ARGV);\nexit $retval if $retval != 0;\n\nmy $i = 1;\nfor(glob('*/scattered.interval_list')) {\n #create unique names and relocate all the scattered intervals to a single directory\n File::Copy::move($_, qq{$i.interval_list});\n $i++\n}\n" ; cwl:entryname "split_interval_list_helper.pl" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "use File::Copy;\n\nmy $retval = system('/usr/bin/java', '-jar', '/usr/picard/picard.jar', 'IntervalListTools', @ARGV);\nexit $retval if $retval != 0;\n\nmy $i = 1;\nfor(glob('*/scattered.interval_list')) {\n #create unique names and relocate all the scattered intervals to a single directory\n File::Copy::move($_, qq{$i.interval_list});\n $i++\n}\n" ; cwl:entryname "split_interval_list_helper.pl" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "snv" . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--normalBam=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "Samtools: merge" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "$(inputs.name).merged.bam" [ CommandLineBinding:prefix "--threads" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( "$(inputs.name).merged.bam" [ CommandLineBinding:prefix "--threads" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "merge" ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "merge" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . cwl:source . sld:type xsd:boolean , sld:null . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:default false . cwl:in , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . cwl:default true . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:default false . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext === \".gz\"){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext === \".gz\"){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext === \".gz\"){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext === \".gz\"){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . rdfs:label "a file with a label" ; sld:fields , ; sld:type sld:record . cwl:valueFrom "pindel" . cwl:source . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] . cwl:in , ; cwl:out ; cwl:run . sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:label "Annotation file type" ; sld:symbols , , , , ; sld:type sld:enum . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:default true . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:default 1e-01 ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$((self.secondaryFiles !== undefined) ? self.secondaryFiles.find(function(x) { return x.nameext === \".dict\" }) : self.replace(/.fa$/,\".dict\") )" . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "normal" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:valueFrom "somatic_snvs" . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect HS metrics" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type xsd:int , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "--llr-threshold" ] ; sld:type xsd:float . a cwl:Workflow ; rdfs:label "pindel parallel workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self)_filtered" . cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1" ; cwl:default 0 ; sld:type xsd:float . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "target-$(self.label)" . cwl:source . cwl:inputBinding [ CommandLineBinding:position -7 ] ; cwl:inputBinding [ CommandLineBinding:position -7 ] ; sld:type xsd:string . cwl:valueFrom "somatic_hc_snvs" . sld:fields , , , , , ; sld:type sld:record . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; sld:type cwl:File . cwl:default "MarkedSorted.bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . rdfs:comment "Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure." ; cwl:default 5 ; sld:type xsd:float . cwl:default 400 ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . rdfs:comment "ensembl version - Must be present in the cache directory. Example: '95'" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--cache_version" ] ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.snvs.vcf.gz" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position -1 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:valueFrom "ALL_READS" . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.file)" . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; sld:type cwl:File , xsd:string , sld:null . cwl:valueFrom "ALL_READS" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf_summary.html" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "False Positive filter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:in , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:label "List of VCF fields to annotate" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "run bam-readcount" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/python" "bam_readcount_helper.py" ) ; cwl:baseCommand ( "/usr/bin/python" "bam_readcount_helper.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.1.1" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.1.1" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/env python\n\nimport sys\nimport os\nfrom cyvcf2 import VCF\nimport tempfile\nimport csv\nfrom subprocess import Popen, PIPE\n\ndef generate_region_list(hash):\n fh = tempfile.NamedTemporaryFile('w', delete=False)\n writer = csv.writer(fh, delimiter='\\t')\n for chr, positions in hash.items():\n for pos in sorted(positions.keys()):\n writer.writerow([chr, pos, pos])\n fh.close()\n return fh.name\n\ndef filter_sites_in_hash(region_list, bam_file, ref_fasta, prefixed_sample, output_dir, insertion_centric, map_qual, base_qual):\n bam_readcount_cmd = ['/usr/bin/bam-readcount', '-f', ref_fasta, '-l', region_list, '-w', '0', '-b', str(base_qual), '-q', str(map_qual)]\n if insertion_centric:\n bam_readcount_cmd.append('-i')\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n else:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n bam_readcount_cmd.append(bam_file)\n execution = Popen(bam_readcount_cmd, stdout=PIPE, stderr=PIPE)\n stdout, stderr = execution.communicate()\n if execution.returncode == 0:\n with open(output_file, 'wb') as output_fh:\n output_fh.write(stdout)\n else:\n sys.exit(stderr)\n\n#initializing these with default values\nmin_base_qual = 20\nmin_mapping_qual = 0\n\nif len(sys.argv) == 7:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir)= sys.argv\nelif len(sys.argv) == 8:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual)= sys.argv\nelif len(sys.argv) == 9: #elif instead of else for explicit safety\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual, min_mapping_qual)= sys.argv\n\nif prefix == 'NOPREFIX':\n prefixed_sample = sample\nelse:\n prefixed_sample = '_'.join([prefix, sample])\n\nvcf_file = VCF(vcf_filename)\nsample_index = vcf_file.samples.index(sample)\n\nrc_for_indel = {}\nrc_for_snp = {}\nfor variant in vcf_file:\n ref = variant.REF\n chr = variant.CHROM\n start = variant.start\n end = variant.end\n pos = variant.POS\n for var in variant.ALT:\n if len(ref) > 1 or len(var) > 1:\n #it's an indel or mnp\n if len(ref) == len(var) or (len(ref) > 1 and len(var) > 1):\n sys.stderr.write(\"Complex variant or MNP will be skipped: %s\\t%s\\t%s\\t%s\\n\" % (chr, pos, ref , var))\n continue\n elif len(ref) > len(var):\n #it's a deletion\n pos += 1\n unmodified_ref = ref\n ref = unmodified_ref[1]\n var = \"-%s\" % unmodified_ref[1:]\n else:\n #it's an insertion\n var = \"+%s\" % var[1:]\n if chr not in rc_for_indel:\n rc_for_indel[chr] = {}\n if pos not in rc_for_indel[chr]:\n rc_for_indel[chr][pos] = {}\n if ref not in rc_for_indel[chr][pos]:\n rc_for_indel[chr][pos][ref] = {}\n rc_for_indel[chr][pos][ref] = variant\n else:\n #it's a SNP\n if chr not in rc_for_snp:\n rc_for_snp[chr] = {}\n if pos not in rc_for_snp[chr]:\n rc_for_snp[chr][pos] = {}\n if ref not in rc_for_snp[chr][pos]:\n rc_for_snp[chr][pos][ref] = {}\n rc_for_snp[chr][pos][ref] = variant\n\nif len(rc_for_snp.keys()) > 0:\n region_file = generate_region_list(rc_for_snp)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, False, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n open(output_file, 'w').close()\n\nif len(rc_for_indel.keys()) > 0:\n region_file = generate_region_list(rc_for_indel)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, True, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n open(output_file, 'w').close()\n" ; cwl:entryname "bam_readcount_helper.py" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/env python\n\nimport sys\nimport os\nfrom cyvcf2 import VCF\nimport tempfile\nimport csv\nfrom subprocess import Popen, PIPE\n\ndef generate_region_list(hash):\n fh = tempfile.NamedTemporaryFile('w', delete=False)\n writer = csv.writer(fh, delimiter='\\t')\n for chr, positions in hash.items():\n for pos in sorted(positions.keys()):\n writer.writerow([chr, pos, pos])\n fh.close()\n return fh.name\n\ndef filter_sites_in_hash(region_list, bam_file, ref_fasta, prefixed_sample, output_dir, insertion_centric, map_qual, base_qual):\n bam_readcount_cmd = ['/usr/bin/bam-readcount', '-f', ref_fasta, '-l', region_list, '-w', '0', '-b', str(base_qual), '-q', str(map_qual)]\n if insertion_centric:\n bam_readcount_cmd.append('-i')\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n else:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n bam_readcount_cmd.append(bam_file)\n execution = Popen(bam_readcount_cmd, stdout=PIPE, stderr=PIPE)\n stdout, stderr = execution.communicate()\n if execution.returncode == 0:\n with open(output_file, 'wb') as output_fh:\n output_fh.write(stdout)\n else:\n sys.exit(stderr)\n\n#initializing these with default values\nmin_base_qual = 20\nmin_mapping_qual = 0\n\nif len(sys.argv) == 7:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir)= sys.argv\nelif len(sys.argv) == 8:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual)= sys.argv\nelif len(sys.argv) == 9: #elif instead of else for explicit safety\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual, min_mapping_qual)= sys.argv\n\nif prefix == 'NOPREFIX':\n prefixed_sample = sample\nelse:\n prefixed_sample = '_'.join([prefix, sample])\n\nvcf_file = VCF(vcf_filename)\nsample_index = vcf_file.samples.index(sample)\n\nrc_for_indel = {}\nrc_for_snp = {}\nfor variant in vcf_file:\n ref = variant.REF\n chr = variant.CHROM\n start = variant.start\n end = variant.end\n pos = variant.POS\n for var in variant.ALT:\n if len(ref) > 1 or len(var) > 1:\n #it's an indel or mnp\n if len(ref) == len(var) or (len(ref) > 1 and len(var) > 1):\n sys.stderr.write(\"Complex variant or MNP will be skipped: %s\\t%s\\t%s\\t%s\\n\" % (chr, pos, ref , var))\n continue\n elif len(ref) > len(var):\n #it's a deletion\n pos += 1\n unmodified_ref = ref\n ref = unmodified_ref[1]\n var = \"-%s\" % unmodified_ref[1:]\n else:\n #it's an insertion\n var = \"+%s\" % var[1:]\n if chr not in rc_for_indel:\n rc_for_indel[chr] = {}\n if pos not in rc_for_indel[chr]:\n rc_for_indel[chr][pos] = {}\n if ref not in rc_for_indel[chr][pos]:\n rc_for_indel[chr][pos][ref] = {}\n rc_for_indel[chr][pos][ref] = variant\n else:\n #it's a SNP\n if chr not in rc_for_snp:\n rc_for_snp[chr] = {}\n if pos not in rc_for_snp[chr]:\n rc_for_snp[chr][pos] = {}\n if ref not in rc_for_snp[chr][pos]:\n rc_for_snp[chr][pos][ref] = {}\n rc_for_snp[chr][pos][ref] = variant\n\nif len(rc_for_snp.keys()) > 0:\n region_file = generate_region_list(rc_for_snp)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, False, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n open(output_file, 'w').close()\n\nif len(rc_for_indel.keys()) > 0:\n region_file = generate_region_list(rc_for_indel)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, True, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n open(output_file, 'w').close()\n" ; cwl:entryname "bam_readcount_helper.py" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.sample)_bam_readcount.tsv" . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--tumorBam=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default false . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -8 ] ; cwl:inputBinding [ CommandLineBinding:position -8 ] ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--mask" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--mask" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . rdfs:comment "scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs" ; sld:type xsd:int . cwl:source . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "samtools index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:default "variants" ; sld:type xsd:string , sld:null . rdfs:label "custom annotation file to be used by vep" ; sld:fields , , ; sld:type sld:record . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max-normal-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max-normal-freq" ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--variant:strelka" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:source . sld:type xsd:float , sld:null . a cwl:Workflow ; rdfs:label "exome alignment and somatic variant detection" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$( (self.secondaryFiles !== undefined) ? self.secondaryFiles.find(function(x) { return x.nameext === \".dict\" }) : self.replace(/.fa$/,\".dict\") )" . cwl:source . cwl:source . cwl:default 400 ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/bin/cat" ) ; 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 "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "per_chromosome_pindel.out" . cwl:default "final.bam" ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:default false ; sld:type xsd:boolean . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; sld:type cwl:File . cwl:default 5e-02 ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . sld:type sld:null ; sld:type [ rdfs:label "custom type, check types directory for input format" ; cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n return [self.annotation.check_existing ? '--check_existing' : '',\n '--custom',\n [self.annotation.file.path,\n self.annotation.name,\n self.annotation.data_format,\n self.method,\n self.force_report_coordinates ? 1 : 0,\n self.annotation.vcf_fields ? self.annotation.vcf_fields : ''\n ].filter(String).join(',')\n ].filter(String)\n}\n" ] ; sld:items ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "strelka workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . a cwl:CommandLineTool ; rdfs:label "expand interval list regions by a given number of basepairs" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)/$(inputs.interval_list.nameroot).expanded.interval_list" ] "UNIQUE=TRUE" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx3g" "-jar" "/usr/picard/picard.jar" "IntervalListTools" ) ; 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 "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--exome" ] ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . sld:type xsd:string . sld:type xsd:float . cwl:source . cwl:source . cwl:in , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:float . cwl:source . rdfs:comment "The effective coverage of capture products generally extends out beyond the actual regions\ntargeted. This parameter allows variants to be called in these wingspan regions, extending\nthis many base pairs from each side of the target regions.\n" ; rdfs:label "target_interval_padding: number of bp flanking each target region in which to allow variant calls" ; cwl:default 100 ; sld:type xsd:int . sld:type xsd:int , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "cle_annotated_vcf_filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docm_and_coding_indel_selection.pl" ) ; 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 "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "add bam_readcount info to vcf" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "output.indel.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "mapq_filtered.vcf.gz" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source , . a cwl:CommandLineTool ; rdfs:label "Ensembl Variant Effect Predictor" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.vcf.nameroot)_annotated.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v1" ] . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "create filtered VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--maskName" "processSomatic" "--filterNotInMask" "-o" [ cwl:valueFrom "$(runtime.outdir)/output.vcf.gz" ] ) ; cwl:arguments ( "--maskName" "processSomatic" "--filterNotInMask" "-o" [ cwl:valueFrom "$(runtime.outdir)/output.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . sld:type xsd:string . cwl:source . a cwl:Workflow ; rdfs:label "Apply filters to VCF file" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . cwl:valueFrom "ALL_READS" . cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type xsd:string , sld:null . cwl:source , . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:default "tumor" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position -6 ] ; cwl:inputBinding [ CommandLineBinding:position -6 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . sld:type xsd:string . cwl:in , , , , , , , , , , , ; cwl:out , , , , , , , , , , ; cwl:run . cwl:source . sld:type xsd:int , sld:null . cwl:default false ; sld:type xsd:boolean . cwl:source . cwl:default "fpfilter" ; sld:type xsd:string , sld:null . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:default 400 ; sld:type xsd:int . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "Exome QC workflow" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , , , , , , , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source ; cwl:valueFrom "summary-$(self.label)" . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.indels.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:default 9.9e-01 ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type xsd:float , sld:null . a cwl:CommandLineTool ; rdfs:label "CombineVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "mutect,varscan,strelka,pindel" "-o" [ cwl:valueFrom "$(runtime.outdir)/combined.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/split_interval_list_to_bed_helper.pl" ) ; 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 "mgibio/cle:v1.4.2" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ] . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:default "NOPREFIX" ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type xsd:string , sld:null . cwl:source . cwl:default 1 ; sld:type xsd:int . cwl:in , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:source . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out , , , , , ; cwl:run . cwl:source . cwl:source . sld:type xsd:float . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "remove END INFO tags" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-x" "INFO/END" "-Oz" "-o" [ cwl:valueFrom "$(runtime.outdir)/pindel.noend.vcf.gz" ] ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "annotate" ) ; 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 "mgibio/bcftools-cwl:1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-j" ] ; sld:type cwl:File , sld:null . cwl:valueFrom "somatic_indels" . a cwl:Workflow ; rdfs:label "Unaligned bam to sorted, markduped bam" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "vcf index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead." ; rdfs:label "Staged Renamer" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] . rdfs:label "File to be used for annotation, include index file" ; sld:type cwl:File . cwl:default 5e-02 ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; sld:type xsd:float , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect insert size metrics" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] "H=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] "H=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--variant:pindel" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "Consequence" , "Feature" , "SYMBOL" , "HGVSp" , "HGVSc" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; sld:type cwl:File . cwl:in , , , , , , , , , , , ; cwl:out , ; cwl:run . sld:type . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "TUMOR" . rdfs:comment "fraction of tumor present in the normal sample (range 0 to 1) - default 0" ; cwl:inputBinding [ CommandLineBinding:position -5 ; CommandLineBinding:prefix "--normal-contamination-rate" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-f" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "PADDING=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . a cwl:Workflow ; rdfs:label "varscan somatic 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:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "strelka 2.9.9" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "$(inputs.cpu_reserved)" ] [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docker_helper.pl" ) ; 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:coresMin 4 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/strelka-cwl:2.9.9" ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Sanitize a VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "HS Metrics workflow" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] . sld:type cwl:File , sld:null . sld:type cwl:File . cwl:valueFrom "roi" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:float . cwl:source . sld:type xsd:boolean , sld:null . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "flag_pick" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:outputBinding [ CommandOutputBinding:glob "all_TD" ] ; sld:type cwl:File . cwl:default 50 ; sld:type xsd:int . sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source , , , , . a cwl:CommandLineTool ; rdfs:label "Mutect2 (GATK 4)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "mutect.vcf.gz" ] ) ; cwl:baseCommand ( "/bin/bash" "Mutect2.sh" ) ; 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 "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\nexport tumor_bam=\"$3\"\nexport normal_bam=\"$4\"\n\nTUMOR=`perl -e 'my $header_str = qx(samtools view -H $ENV{tumor_bam}); my ($sample_name) = $header_str =~ /SM:([ -~]+)/; print $sample_name'` #Extracting the sample name from the TUMOR bam.\nNORMAL=`perl -e 'my $header_str = qx(samtools view -H $ENV{normal_bam}); my ($sample_name) = $header_str =~ /SM:([ -~]+)/; print $sample_name'` #Extracting the sample name from the NORMAL bam.\n/gatk/gatk Mutect2 --java-options \"-Xmx20g\" -O $1 -R $2 -I $3 -tumor \"$TUMOR\" -I $4 -normal \"$NORMAL\" -L $5 #Running Mutect2.\n/gatk/gatk FilterMutectCalls -R $2 -V mutect.vcf.gz -O mutect.filtered.vcf.gz #Running FilterMutectCalls on the output vcf.\n" ; cwl:entryname "Mutect2.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 32000 ; ResourceRequirement:tmpdirMin 100000 ] . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default "AC" , "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" , "AF" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:default "queryname" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "BAM to CRAM conversion" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "view" "-C" ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "view" "-C" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:stdout "$(inputs.bam.nameroot).cram" . cwl:source . a cwl:CommandLineTool ; rdfs:label "add VEP annotation to report" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:default "Consequence" , "Feature" , "SYMBOL" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:default "Wildtype" , "Downstream" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 4.1.8.1)" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:valueFrom "annotated_filtered.vcf" . sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; sld:type cwl:File . cwl:default false . sld:type cwl:File . sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/bin/grep" "ChrID" "/dev/stdin" ) ; cwl:baseCommand ( "/bin/cat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "all_region_pindel.head" . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:default "NORMAL" . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . a cwl:CommandLineTool ; rdfs:label "samtools index cram" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.cram.basename)" "$(runtime.outdir)/$(inputs.cram.basename).crai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.cram.basename).crai" "$(runtime.outdir)/$(inputs.cram.nameroot).crai" ) ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.cram.basename)" "$(runtime.outdir)/$(inputs.cram.basename).crai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.cram.basename).crai" "$(runtime.outdir)/$(inputs.cram.nameroot).crai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.cram; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.cram; delete f.secondaryFiles; return f }" ] . rdfs:label "Used as key for new VEP annotation" ; sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; sld:type sld:null , cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$((self.secondaryFiles !== undefined) ? self.secondaryFiles.find(function(x) { return x.nameext === \".dict\" }) : self.replace(/.fa$/,\".dict\") )" . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:label "samtools flagstat" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "flagstat" ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "flagstat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.bam.basename).flagstat" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "interval_list.bed" ] ; sld:type cwl:File . rdfs:comment "Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure." ; cwl:default 5 ; sld:type xsd:float . sld:type xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "Detect Variants 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:SubworkflowFeatureRequirement ] . cwl:default "select_variants" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , , , , , , , , , , ; cwl:out , , , , , , , , , , ; cwl:run . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . sld:type cwl:Directory , xsd:string . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; sld:type cwl:Directory , xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type xsd:float . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; sld:type cwl:File . cwl:default "AC" , "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" , "AF" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "pindel.out.vcf" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "mutect parallel workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "all_region_pindel.head" ] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type cwl:File . rdfs:comment "tumor cellularity fraction (range 0 to 1) - default 1" ; cwl:inputBinding [ CommandLineBinding:position -4 ; CommandLineBinding:prefix "--tumor-purity" ] ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self).bam" . cwl:source . sld:type xsd:float , sld:null . a cwl:CommandLineTool ; rdfs:label "filter variants at sites below a given sequence depth in each sample" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(runtime.outdir)/depth_filtered.vcf" ] ) ; cwl:baseCommand ( "/opt/conda/bin/python3" "/usr/bin/depth_filter.py" ) ; 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 "mgibio/depth-filter:0.1.2" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:int , sld:null . rdfs:label "Identify known variants colocated with input variant" ; sld:type xsd:boolean . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] .