@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: .
a cwl:CommandLineTool ;
rdfs:label "Mark duplicates and Sort" ;
ns1:original_cwlVersion "v1.0" ;
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:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs , ;
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 $3 /dev/stdin\nfi\n" ;
cwl:entryname "markduplicates_helper.sh"
]
] .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "sort BAM by name" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-t"
[ cwl:valueFrom "$(runtime.cores)" ]
"-m" "22G" "-n" "-o"
[ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ]
) ;
cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin 24000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4"
] .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:default 20 ;
cwl:inputBinding [ CommandLineBinding:position
-2 ] ;
sld:type xsd:int , sld:null .
cwl:in , , , ;
cwl:out ;
cwl:run .
rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--assembly"
] ;
sld:type xsd:string .
cwl:default "Consequence" , "Feature_type" , "SYMBOL" , "PHENO" , "HGVSc" , "Feature" , "gnomADe_AF" , "CDS_position" , "Codons" , "HGNC_ID" , "SOMATIC" , "cDNA_position" , "Existing_variation" , "CLIN_SIG" , "Amino_acids" , "HGVSp" , "Protein_position" ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
cwl:default "select_variants" ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"${\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 1e-01 ;
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type xsd:float , sld:null .
cwl:source .
a cwl:Workflow ;
rdfs:label "bgzip and index VCF" ;
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 , sld:null .
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
] .
cwl:source .
cwl:source .
cwl:source .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:default "MarkedSorted.bam" ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:string , sld:null .
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:default 9.9e-01 ;
sld:type xsd:float , sld:null .
sld:type cwl:File .
sld:type sld:null ;
sld:type [ rdfs:label "custom type, check types directory for input format" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
cwl:valueFrom "${\n return [self.annotation.check_existing ? '--check_existing' : '',\n '--custom',\n [self.annotation.file.path,\n self.annotation.name,\n self.annotation.data_format,\n self.method,\n self.force_report_coordinates ? 1 : 0,\n self.annotation.vcf_fields ? self.annotation.vcf_fields : ''\n ].filter(String).join(',')\n ].filter(String)\n}\n"
] ;
sld:items ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this" ;
rdfs:label "align with bwa_mem and tag" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-n" ;
cwl:valueFrom "$(runtime.cores)"
]
) ;
cwl:baseCommand ( "/bin/bash" "sequence_alignment_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:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\nset -o nounset\n\nwhile getopts \"b:?1:?2:?g:r:n:\" opt; do\n case \"$opt\" in\n b)\n MODE=bam\n BAM=\"$OPTARG\"\n ;;\n 1)\n MODE=fastq\n FASTQ1=\"$OPTARG\"\n ;;\n 2) \n MODE=fastq\n FASTQ2=\"$OPTARG\"\n ;;\n g)\n READGROUP=\"$OPTARG\"\n ;;\n r)\n REFERENCE=\"$OPTARG\"\n ;;\n n)\n NTHREADS=\"$OPTARG\"\n ;;\n esac\ndone\n\nif [[ \"$MODE\" == 'fastq' ]]; then\n /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -R \"$READGROUP\" \"$REFERENCE\" \"$FASTQ1\" \"$FASTQ2\" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\nfi\nif [[ \"$MODE\" == 'bam' ]]; then\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\nfi\n" ;
cwl:entryname "sequence_alignment_helper.sh"
]
] ;
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:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:stdout "refAlign.bam" .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-b" ] ;
sld:type cwl:File , sld:null .
cwl:source .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
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:source .
cwl:outputSource ;
sld:type cwl:File .
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type xsd:string .
cwl:source .
cwl:in , , , , , , ;
cwl:out , , , , ;
cwl:run .
cwl:source .
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 "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
sld:type xsd:boolean , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"interval_list.bed" ] ;
sld:type cwl:File .
cwl:default "TUMOR" ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--sample"
] ;
sld:type xsd:string , sld:null .
cwl:default "queryname" ;
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type xsd:string .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type [ sld:items ;
sld:type sld:array
] .
sld:type cwl:File .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "collect gc bias metrics" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).GcBiasMetrics.txt" ]
"CHART="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).GcBiasMetricsChart.pdf" ]
"S="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).GcBiasMetricsSummary.txt" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectGcBiasMetrics" ) ;
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 18000
] .
sld:type cwl:File .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
cwl:in , , , ;
cwl:out , ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"annotated.vcf_summary.html" ] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:default "DNA" .
sld:type xsd:float , sld:null .
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
] .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
sld:type xsd:string .
rdfs:label "sequence data with readgroup information" ;
sld:fields , ;
sld:type sld:record .
rdfs:comment "the unaligned sequence data with readgroup information" ;
sld:type .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File .
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:source .
cwl:inputBinding [ CommandLineBinding:prefix
"BAIT_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"BAIT_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"BAIT_INTERVALS=" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--synonyms"
] ;
sld:type cwl:File , sld:null .
cwl:default 2 ;
cwl:inputBinding [ CommandLineBinding:position
6 ] ;
sld:type xsd:int , sld:null .
cwl:default "final" ;
sld:type xsd:string , sld:null .
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ;
sld:type xsd:string .
rdfs:label "Identify known variants colocated with input variant" ;
sld:type xsd:boolean .
cwl:source .
sld:type xsd:string .
rdfs:label "Use this annotation for gnomad filtering?" ;
sld:type xsd:boolean , sld:null .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:prefix
"TARGET_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"TARGET_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"TARGET_INTERVALS=" ] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type [ sld:symbols , ;
sld:type sld:enum
] .
cwl:source ;
cwl:valueFrom "$(self.file)" .
cwl:source .
cwl:valueFrom "ALL_READS" .
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "samtools index" ;
ns1:original_cwlVersion "v1.0" ;
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 ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs