@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: . @prefix ExpressionTool: . rdfs:comment "include genotypes from this sample" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-bqsr" ] ; sld:type cwl:File . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:default 2 . cwl:in , , , ; cwl:out ; cwl:run . cwl:in , , , , ; cwl:out ; cwl:run . cwl:in , , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . 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:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Used to generate the output file name" ; cwl:default "SURVIVOR-sv-merged.vcf" ; cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type xsd:string , sld:null . sld:fields , , , , , ; sld:type sld:record . sld:fields ; sld:type sld:record . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).GcBiasMetricsChart.pdf" ] ; sld:type cwl:File . sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:source ; cwl:valueFrom "summary-$(self.label)" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Run CNVnator to calculate copy number variations in WGS samples" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/bin/bash" "run_cnvnator.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/cnvnator-cwl:0.4" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 20000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\n\n#set up the environment\nsource /opt/root/bin/thisroot.sh\n\nset -eou pipefail\n\n# set vars\nBAM=\"$1\"\nBIN_SIZE=\"$2\"\nCHROMOSOMES=\"$3\"\nREFERENCE=\"$4\"\nSAMPLE=\"$5\"\n\n# create directory to store fasta files. CNVnator wants chromosomes in individual files\n# while with later versions of CNVnator these steps will accept a fasta.gz file the cnvnator2VCF.pl will not\nmkdir FASTA_CHRS\nawk 'BEGIN { CHROM=\"\" } { if ($1~\"^>\") CHROM=substr($1,2); print $0 > \"FASTA_CHRS/\"CHROM\".fa\" }' \"$REFERENCE\"\n\n# extract read mapping from input bam(single sample)\ncnvnator -root \"$SAMPLE.root\" -tree \"$BAM\" -chrom $CHROMOSOMES\n# generate read depth histogram\ncnvnator -root \"$SAMPLE.root\" -his \"$BIN_SIZE\" -d FASTA_CHRS/ -chrom $CHROMOSOMES\n# calculate statistics\ncnvnator -root \"$SAMPLE.root\" -stat \"$BIN_SIZE\" -chrom $CHROMOSOMES\n# read depth signal partitioning\ncnvnator -root \"$SAMPLE.root\" -partition \"$BIN_SIZE\" -chrom $CHROMOSOMES\n# cnv calling\ncnvnator -root \"$SAMPLE.root\" -call \"$BIN_SIZE\" -chrom $CHROMOSOMES > \"$SAMPLE.CNVnator.cn\"\n\n# convert to vcf\ncnvnator2VCF.pl -reference \"$REFERENCE\" \"$SAMPLE.CNVnator.cn\" FASTA_CHRS/ > \"$SAMPLE.CNVnator.vcf\"\nexit 0\n" ; cwl:entryname "run_cnvnator.sh" ] ] . sld:type xsd:int . cwl:source ; cwl:valueFrom "##disclaimer=$(self)" . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , ; cwl:run . cwl:source . cwl:source . cwl:in , , , ; cwl:out , , ; cwl:run . rdfs:comment "Depth for duplications must be greater than this cutoff to pass the filter." ; cwl:default 1.25e+00 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:double , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . rdfs:comment "method for filtering/merging neighboring copy number segments" ; cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--filter" ] ; sld:type sld:null ; sld:type [ sld:symbols , , , ; sld:type sld:enum ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-SVinputFile" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-SVinputFile" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default false . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).cnr" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type [ sld:symbols , , ; sld:type sld:enum ] . sld:type , . sld:type xsd:int , sld:null . rdfs:comment "output vcf file name" ; cwl:default "filtered_sv_size.vcf" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; sld:type cwl:File . cwl:source . rdfs:comment "Used for naming the output file" ; cwl:default "SV" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--name" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . cwl:valueFrom "annotated.filtered.tsv" . sld:type xsd:boolean . cwl:source ; cwl:valueFrom "##disclaimer=$(self)" . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:int , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:double , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name).bam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "GATK HaplotypeCaller" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "HaplotypeCaller" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:default "cnvkit" . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:in , , , , , , ; cwl:out , , , , , ; cwl:run . rdfs:comment "if true, outputs assembled contig sequences in final VCF files, in the INFO field CONTIG" ; cwl:inputBinding [ CommandLineBinding:position -7 ; CommandLineBinding:prefix "--outputContig" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "Insert an arbitrary string at a specific line of a file" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-v" [ cwl:valueFrom "n=$(inputs.line_number)" ] "-v" [ cwl:valueFrom "s=$(inputs.some_text)" ] "NR == n {print s} {print}" ) ; cwl:arguments ( "-v" [ cwl:valueFrom "n=$(inputs.line_number)" ] "-v" [ cwl:valueFrom "s=$(inputs.some_text)" ] "NR == n {print s} {print}" ) ; cwl:arguments ( "-v" [ cwl:valueFrom "n=$(inputs.line_number)" ] "-v" [ cwl:valueFrom "s=$(inputs.some_text)" ] "NR == n {print s} {print}" ) ; cwl:arguments ( "-v" [ cwl:valueFrom "n=$(inputs.line_number)" ] "-v" [ cwl:valueFrom "s=$(inputs.some_text)" ] "NR == n {print s} {print}" ) ; cwl:arguments ( "-v" [ cwl:valueFrom "n=$(inputs.line_number)" ] "-v" [ cwl:valueFrom "s=$(inputs.some_text)" ] "NR == n {print s} {print}" ) ; cwl:baseCommand ( "awk" ) ; cwl:baseCommand ( "awk" ) ; cwl:baseCommand ( "awk" ) ; cwl:baseCommand ( "awk" ) ; cwl:baseCommand ( "awk" ) ; 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: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:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:stdout "$(inputs.output_name)" . cwl:source . a cwl:CommandLineTool ; rdfs:label "Custom allele frequency filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v1" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . sld:type xsd:boolean , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 7 ] ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type cwl:File . rdfs:comment "output vcf file name" ; cwl:default "bcftools_merged.vcf.gz" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--output" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "reference.cnn" ] ; sld:type cwl:File , sld:null . rdfs:comment "Normal samples (.bam) used to construct the pooled, paired, or flat reference. If this option is used but no filenames are given, a 'flat' reference will be built. Otherwise, all filenames following this option will be used." ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File , sld:null . sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).cns" ] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:int . rdfs:comment "Array of VCFs to merge SV calls of" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File , sld:null . cwl:source . sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)" . rdfs:comment "the unaligned sequence data with readgroup information" ; sld:type . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:valueFrom "ALL_READS" . sld:type [ sld:items ; sld:type sld:array ] . sld:fields , ; sld:type sld:record . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type xsd:int , sld:null . cwl:default "flag_pick" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:default "bcftools-sv-merged.vcf" . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:run . sld:type [ sld:items ; sld:type sld:array ] . cwl:default "annotated.filtered.final" . cwl:in ; cwl:out ; cwl:run . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--all-CDS" ] ; sld:type xsd:boolean , sld:null . cwl:default "SURVIVOR-sv-merged" . cwl:source . cwl:source . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default "variants" ; sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "bqsr.table" ] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Bin size used to calculate coverage" ; cwl:default 100 ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "annotated.af_filtered.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "min_len" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somaticSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "Sample name used for output file naming" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:default "filtered-bcftools-merged-AnnotSV.tsv" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--output" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:default 5e-02 ; sld:type xsd:float . a cwl:Workflow ; rdfs:label "Filter single sample sv vcf from paired read callers(Manta/Smoove)" ; 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:outputSource ; sld:type cwl:File . cwl:source . cwl:source . 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:arguments ( "-c" ) ; cwl:baseCommand ( "/usr/local/bin/bgzip" ) ; cwl:baseCommand ( "/usr/local/bin/bgzip" ) ; cwl:baseCommand ( "/usr/local/bin/bgzip" ) ; cwl:baseCommand ( "/usr/local/bin/bgzip" ) ; cwl:baseCommand ( "/usr/local/bin/bgzip" ) ; cwl:baseCommand ( "/usr/local/bin/bgzip" ) ; cwl:baseCommand ( "/usr/local/bin/bgzip" ) ; cwl:baseCommand ( "/usr/local/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 ; 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 ; 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:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_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:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:stdout "$(inputs.file.basename).gz" . sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).CNVnator.vcf" ] ; sld:type cwl:File . cwl:in , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "required alternate read abundance percentage to pass" ; cwl:default 1e-01 ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:double , sld:null . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:default "$(inputs.input_file.basename).commented" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:outputSource ; sld:type cwl:File . a cwl:Workflow ; rdfs:comment "Some workflow engines won't stage files in our nested structure, so parse it out here" ; rdfs:label "adapter for sequence_align_and_tag" ; 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:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:default "false" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-s" ] ; sld:type xsd:boolean , sld:null . cwl:default 1 . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--ignore-pass-filter" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".target.bed\";\n if (inputs.bait_intervals) {\n glob_base = inputs.bait_intervals.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "##disclaimer=$(self)" . cwl:source . cwl:source . sld:type , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . a cwl:Workflow ; rdfs:label "WGS QC workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "/opt/AnnotSV_2.1/bin/AnnotSV" "-bedtools" "/usr/bin/bedtools" "-outputDir" "$(runtime.outdir)" ) ; cwl:arguments ( "/opt/AnnotSV_2.1/bin/AnnotSV" "-bedtools" "/usr/bin/bedtools" "-outputDir" "$(runtime.outdir)" ) ; 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/annotsv-cwl:2.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/annotsv-cwl:2.1" ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_size.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_size.sh" ) ; 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/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\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nSV_SIZE=\"$3\"\nFILTER_METHOD=\"$4\"\n\nif [ \"$FILTER_METHOD\" == \"max_len\" ]; then\n echo \"Running filter for max size svs\"\n filter_expression=\"ABS(SVLEN) <= $SV_SIZE\"\nelif [ \"$FILTER_METHOD\" == \"min_len\" ]; then\n echo \"Running filter for min size svs\"\n filter_expression=\"ABS(SVLEN) >= $SV_SIZE\"\nelse\n echo \"Filter method: '$FILTER_METHOD' is not supported for size SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_size.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nSV_SIZE=\"$3\"\nFILTER_METHOD=\"$4\"\n\nif [ \"$FILTER_METHOD\" == \"max_len\" ]; then\n echo \"Running filter for max size svs\"\n filter_expression=\"ABS(SVLEN) <= $SV_SIZE\"\nelif [ \"$FILTER_METHOD\" == \"min_len\" ]; then\n echo \"Running filter for min size svs\"\n filter_expression=\"ABS(SVLEN) >= $SV_SIZE\"\nelse\n echo \"Filter method: '$FILTER_METHOD' is not supported for size SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_size.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).root" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "verify BAM ID" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--out" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ] ) ; cwl:baseCommand ( "/usr/local/bin/verifyBamID" ) ; 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/verify_bam_id-cwl:1.1.3" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . 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 . rdfs:comment "toggles on settings for WES" ; cwl:inputBinding [ CommandLineBinding:position -6 ; CommandLineBinding:prefix "--exome" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File , sld:null . sld:type cwl:File , sld:null . rdfs:comment "bwa-indexed reference file" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type cwl:File , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Minimum size of SVs to merge" ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type xsd:int . cwl:outputSource ; sld:type cwl:File . 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:source . cwl:outputSource ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "wgs alignment with qc" ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] . sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:default false . a cwl:CommandLineTool ; rdfs:label "filter AnnotSV tsv output generated from a bcftools merged vcf" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "python3" "AnnotSV_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 "python:3" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import argparse\nimport csv\nimport sys\n\nparser = argparse.ArgumentParser()\nparser.add_argument('--input', '-i', dest=\"input\", help='input AnnotSV tsv file', required=True, action=\"store\")\nparser.add_argument('--output', '-o', dest=\"output\", help='output tsv file name', required=True, action=\"store\")\nparser.add_argument('--filtering_frequency', dest=\"filtering_frequency\", help=\"frequency to filter with\", action=\"store\", type=float, default=\"0.05\")\nparser.add_argument('--all-CDS', dest=\"CDS\", help=\"Do not require a positive CoDing Sequence overlap\", action=\"store_true\")\nparser.add_argument('--ignore-pass-filter', dest=\"filter\", help=\"Do not require calls to have a PASS filter\", action=\"store_true\")\n\nargs = parser.parse_args()\ninput_file_name = args.input\noutput_file_name = args.output\nfiltering_frequency = args.filtering_frequency\nall_cds = args.CDS\nignore_pass_filter = args.filter\n\nwith open(input_file_name, 'r') as file_in, open(output_file_name, 'w') as file_out:\n file_in = csv.DictReader(file_in, delimiter='\\t')\n file_out = csv.DictWriter(file_out, fieldnames=file_in.fieldnames, delimiter='\\t')\n file_out.writeheader()\n total_sv_count = 0\n pass_sv_count = 0\n for row in file_in:\n total_sv_count += 1\n if(row['AnnotSV type'] == 'split' \\\n and (row['FILTER'] == 'PASS' or ignore_pass_filter) \\\n and (int(row['CDS length']) > 0 or all_cds) \\\n and float(row['IMH_AF']) < filtering_frequency\n and float(row['1000g_max_AF']) < filtering_frequency\n and not(float(row['DGV_LOSS_Frequency']) > filtering_frequency and 'DEL' in row['SV type']) \n and not(float(row['DGV_GAIN_Frequency']) < filtering_frequency and ('DUP' in row['SV type'] or 'INS' in row['SV type']))\n and not(('Manta' in row['ID'] and 'IMPRECISE' in row['INFO']) or (row['QUAL'] != '.' and 'IMPRECISE' in row['INFO'])) ):\n file_out.writerow(row)\n pass_sv_count += 1\n print(\"total sv count:\",total_sv_count)\n print(\"total sv passed count:\",pass_sv_count)\n" ; cwl:entryname "AnnotSV_filter.py" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . rdfs:comment "Minimum number of sv calls needed to be merged" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int . cwl:in , , , ; cwl:out ; cwl:run . 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 "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 26000 ] . sld:type xsd:double , sld:null . cwl:default "wgs" ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "bgzip-compressed, tabix-indexed BED file specifiying regions to which variant analysis will be restricted" ; cwl:inputBinding [ CommandLineBinding:position -5 ; CommandLineBinding:prefix "--callRegions" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; sld:type cwl:File . sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cohort_name)-smoove.genotyped.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:default true . cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; sld:type cwl:File . rdfs:comment "Depth for deletions must be less than this cutoff to pass the filter." ; cwl:default 7.5e-01 ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:double , sld:null . rdfs:comment "select only a certain type of variants" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:default 2 . rdfs:comment "bwa-indexed reference file" ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "Subworkflow to allow calling different SV callers which require bam files as inputs" ; 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:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/candidateSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--input" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "wgs alignment and germline variant detection" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:in , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "output vcf file name" ; cwl:default "filtered_cnv.vcf" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string , sld:null . cwl:default false . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "Insert an arbitrary string at a specific line of a gzipped file" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.input_file.path)" ] [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "awk" "-v" [ cwl:valueFrom "n=$(inputs.line_number)" ] "-v" [ cwl:valueFrom "s=$(inputs.some_text)" ] "NR == n {print s} {print}" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/opt/htslib/bin/bgzip" ) ; cwl:arguments ( [ cwl:valueFrom "$(inputs.input_file.path)" ] [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "awk" "-v" [ cwl:valueFrom "n=$(inputs.line_number)" ] "-v" [ cwl:valueFrom "s=$(inputs.some_text)" ] "NR == n {print s} {print}" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/opt/htslib/bin/bgzip" ) ; cwl:arguments ( [ cwl:valueFrom "$(inputs.input_file.path)" ] [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "awk" "-v" [ cwl:valueFrom "n=$(inputs.line_number)" ] "-v" [ cwl:valueFrom "s=$(inputs.some_text)" ] "NR == n {print s} {print}" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/opt/htslib/bin/bgzip" ) ; cwl:arguments ( [ cwl:valueFrom "$(inputs.input_file.path)" ] [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "awk" "-v" [ cwl:valueFrom "n=$(inputs.line_number)" ] "-v" [ cwl:valueFrom "s=$(inputs.some_text)" ] "NR == n {print s} {print}" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "zcat" ) ; cwl:baseCommand ( "zcat" ) ; cwl:baseCommand ( "zcat" ) ; cwl:baseCommand ( "zcat" ) ; 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 ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:stdout "$(inputs.output_name)" . cwl:source . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "assume genotypes at missing sites are 0/0" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--missing-to-ref" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; sld:type cwl:File . sld:type xsd:double , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; sld:type cwl:File , sld:null . sld:type cwl:File . cwl:valueFrom "ALL_READS" . sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "merged.bam" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Reference used to generate the bams" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--fasta" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default "filtered_cnvnator.vcf" . cwl:default "bcftools-sv-merged" . sld:type xsd:boolean , sld:null . cwl:source . cwl:source ; cwl:valueFrom "#$(self)" . sld:type xsd:string . cwl:source . rdfs:comment "if present in variant, number of alternate split reads support needed to pass" ; cwl:default 2 ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:int , sld:null . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GQB" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "Run Smoove v0.1.6" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "call" "--processes" "$(runtime.cores)" "-F" ) ; cwl:baseCommand ( "/usr/bin/smoove" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 20000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/smoove:0.2.6--0" ] . cwl:default 2 . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 4.1.8.1)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] . rdfs:comment "Bed file used to exclude regions" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude" ] ; sld:type cwl:File , sld:null . sld:type cwl:File , sld:null . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position -4 ; CommandLineBinding:prefix "--referenceFasta" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . a cwl:Workflow ; rdfs:label "scatter GATK HaplotypeCaller over intervals" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(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" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:label "List of VCF fields to annotate" ; 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 ] . cwl:default "variants" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "BAM to CRAM conversion" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools" "view" "-C" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.bam.nameroot).cram" . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . sld:type , sld:null . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_tsv_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_tsv_name)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".targetcoverage.cnn\";\n if (inputs.normal_bam) {\n glob_base = inputs.normal_bam.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:double , sld:null . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Array of bams to run through lumpy, can be single or small cohort" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genotype" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source ; cwl:valueFrom "${\n if(self){\n for(var i=0; i cwl:source . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . a cwl:CommandLineTool ; rdfs:label "cgpBigWig Converting BAM to BigWig" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).bw" ] ) ; cwl:baseCommand ( "bam2bw" "-a -F" "1024" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 32000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/cgpbigwig:1.4.0--h93d22ca_0" ] . cwl:default "cnvnator" . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-y" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , , ; cwl:out , , ; cwl:run . sld:type xsd:int , sld:null . 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 . rdfs:comment "output file format" ; cwl:default "z" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--output-type" ] ; sld:type [ sld:symbols , , , ; sld:type sld:enum ] . cwl:source . sld:type xsd:int , sld:null . cwl:source . sld:type xsd:int , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--threads" "$(runtime.cores)" ) ; cwl:arguments ( "--threads" "$(runtime.cores)" ) ; cwl:baseCommand ( "/usr/bin/duphold" ) ; cwl:baseCommand ( "/usr/bin/duphold" ) ; 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/duphold-cwl:0.1.5" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/duphold-cwl:0.1.5" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 10000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 10000 ] . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type xsd:string , sld:null . cwl:default "smoove" . cwl:source . sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Sequencing protocol used for input data" ; cwl:default "hybrid" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--method" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:valueFrom "annotated.filtered.final.tsv" . cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "output vcf basename" ; cwl:default "blocklist_filtered" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:string , sld:null . cwl:source . cwl:default "filtered_smoove.vcf" . rdfs:label "sequence data with readgroup information" ; sld:fields , ; sld:type sld:record . cwl:source . cwl:source . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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: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 $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] . cwl:source . sld:type . rdfs:comment "snps vcf(s) for adding hom/het snp counts found within svs" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 5 ; CommandLineBinding:prefix "-vcfFiles" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 5 ; CommandLineBinding:prefix "-vcfFiles" ] ; sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . rdfs:comment "reference used to align bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--fasta" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--fasta" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . rdfs:comment "Require merged SVs to be of the same type" ; cwl:inputBinding [ CommandLineBinding:position 4 ; cwl:valueFrom "${\n if(inputs.same_type){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:type xsd:int . cwl:source . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . rdfs:comment "maximum number of alternate alleles to genotype" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--max_alternate_alleles" ] ; sld:type xsd:int , sld:null . sld:type xsd:string , sld:null . sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] . cwl:in , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Set up and execute manta" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -1 ; CommandLineBinding:prefix "--runDir" ; cwl:valueFrom "$(runtime.outdir)" ] [ CommandLineBinding:shellQuote false ; cwl:valueFrom "&&" ] "/usr/bin/python" "runWorkflow.py" "-m" "local" [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-j" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/bin/manta/bin/configManta.py" ) ; cwl:cwlVersion ; 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 "mgibio/manta_somatic-cwl:1.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 12 ; ResourceRequirement:ramMin 24000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl:source . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_depth.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_depth.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_depth.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_depth.sh" ) ; 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 ; 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:inputs , , , , ; cwl:outputs ; 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\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nDEL_DEPTH=\"$3\"\nDUP_DEPTH=\"$4\"\nVCF_SOURCE=\"$5\"\n\nif [ \"$VCF_SOURCE\" == \"cnvnator\" ]; then\n echo \"Running filter for cnvnator vcf\"\n filter_expression=\"(natorRD>$DUP_DEPTH | natorRD<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"cnvkit\" ]; then\n echo \"Running filter for cnvkit vcf\"\n filter_expression=\"(FOLD_CHANGE>$DUP_DEPTH | FOLD_CHANGE<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"duphold\" ]; then\n echo \"Running filter for vcf annotated by duphold\"\n filter_expression=\"((SVTYPE='DEL' & FMT/DHFFC[0] < $DEL_DEPTH) | (SVTYPE='DUP' & FMT/DHBFC[0] > $DUP_DEPTH) | SVTYPE='BND' | SVTYPE='INS' | SVTYPE='INV')\"\nelse\n echo \"vcf source: '$VCF_SOURCE' is not supported for SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_depth.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nDEL_DEPTH=\"$3\"\nDUP_DEPTH=\"$4\"\nVCF_SOURCE=\"$5\"\n\nif [ \"$VCF_SOURCE\" == \"cnvnator\" ]; then\n echo \"Running filter for cnvnator vcf\"\n filter_expression=\"(natorRD>$DUP_DEPTH | natorRD<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"cnvkit\" ]; then\n echo \"Running filter for cnvkit vcf\"\n filter_expression=\"(FOLD_CHANGE>$DUP_DEPTH | FOLD_CHANGE<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"duphold\" ]; then\n echo \"Running filter for vcf annotated by duphold\"\n filter_expression=\"((SVTYPE='DEL' & FMT/DHFFC[0] < $DEL_DEPTH) | (SVTYPE='DUP' & FMT/DHBFC[0] > $DUP_DEPTH) | SVTYPE='BND' | SVTYPE='INS' | SVTYPE='INV')\"\nelse\n echo \"vcf source: '$VCF_SOURCE' is not supported for SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_depth.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nDEL_DEPTH=\"$3\"\nDUP_DEPTH=\"$4\"\nVCF_SOURCE=\"$5\"\n\nif [ \"$VCF_SOURCE\" == \"cnvnator\" ]; then\n echo \"Running filter for cnvnator vcf\"\n filter_expression=\"(natorRD>$DUP_DEPTH | natorRD<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"cnvkit\" ]; then\n echo \"Running filter for cnvkit vcf\"\n filter_expression=\"(FOLD_CHANGE>$DUP_DEPTH | FOLD_CHANGE<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"duphold\" ]; then\n echo \"Running filter for vcf annotated by duphold\"\n filter_expression=\"((SVTYPE='DEL' & FMT/DHFFC[0] < $DEL_DEPTH) | (SVTYPE='DUP' & FMT/DHBFC[0] > $DUP_DEPTH) | SVTYPE='BND' | SVTYPE='INS' | SVTYPE='INV')\"\nelse\n echo \"vcf source: '$VCF_SOURCE' is not supported for SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_depth.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nDEL_DEPTH=\"$3\"\nDUP_DEPTH=\"$4\"\nVCF_SOURCE=\"$5\"\n\nif [ \"$VCF_SOURCE\" == \"cnvnator\" ]; then\n echo \"Running filter for cnvnator vcf\"\n filter_expression=\"(natorRD>$DUP_DEPTH | natorRD<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"cnvkit\" ]; then\n echo \"Running filter for cnvkit vcf\"\n filter_expression=\"(FOLD_CHANGE>$DUP_DEPTH | FOLD_CHANGE<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"duphold\" ]; then\n echo \"Running filter for vcf annotated by duphold\"\n filter_expression=\"((SVTYPE='DEL' & FMT/DHFFC[0] < $DEL_DEPTH) | (SVTYPE='DUP' & FMT/DHBFC[0] > $DUP_DEPTH) | SVTYPE='BND' | SVTYPE='INS' | SVTYPE='INV')\"\nelse\n echo \"vcf source: '$VCF_SOURCE' is not supported for SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_depth.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--species" ] ; sld:type xsd:string . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:boolean , sld:null . 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 [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/candidateSmallIndels.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:boolean , sld:null . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . a cwl:Workflow ; rdfs:label "Merge, annotate, and generate a TSV for SVs" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . rdfs:comment "Estimate distance based on the size of SV" ; cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n if(inputs.estimate_sv_distance){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . cwl:in , , , , , , , , , , ; cwl:out ; cwl:run . sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . a cwl:Workflow ; rdfs:label "Raw sequence data to BQSR" ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/diploidSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "Run SURVIVOR to merge SV calls" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/bin/bash" "/usr/bin/survivor_merge_helper.sh" ) ; cwl:cwlVersion ; 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:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 2000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/survivor-cwl:1.0.6.2" ] . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . rdfs:comment "aligned bam/cram file" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bam" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bam" ] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source , , , . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default true . cwl:outputSource ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "HS Metrics 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . 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 "v1.2" ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "output.g.vcf.gz" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "-O" ] ; sld:type xsd:string . a cwl:Workflow ; rdfs:label "Filter single sample sv vcf from depth callers(cnvkit/cnvnator)" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; 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:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:double , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-ERC" ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . sld:type xsd:boolean . sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).antitargetcoverage.cnn" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:in , , , , , , , , , ; cwl:out , , , , ; cwl:run . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . rdfs:label "Annotation file type" ; sld:symbols , , , , ; sld:type sld:enum . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n return [\n \"--filter\",\n [\n inputs.field_name, \"<\", inputs.maximum_population_allele_frequency,\n \"or not\", inputs.field_name\n ].join(\" \")\n ]\n}\n" ] ; sld:type xsd:float . cwl:source . sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type cwl:File . cwl:default "cnvnator" . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-1" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:source . cwl:source ; cwl:valueFrom "target-$(self.label)" . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:comment "array of plugins to use when running vep" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:int . cwl:in , ; cwl:out ; cwl:run . 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 "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; sld:type xsd:boolean , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(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).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; sld:type cwl:File , sld:null . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . rdfs:label "trimming adapter file and parameters" ; sld:fields , ; sld:type sld:record . cwl:source . cwl:source . cwl:in , , ; cwl:out , ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . rdfs:comment "sv vcf file to annotate" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--vcf" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--vcf" ] ; sld:type cwl:File . sld:type xsd:float . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)" . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "samtools flagstat" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools" "flagstat" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.bam.basename).flagstat" . cwl:in , , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.basename)" . sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--cnr" ] ; sld:type cwl:File , sld:null . sld:type xsd:int . cwl:source . rdfs:comment "Average size of split target bins (results are approximate)" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--target-avg-size" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:in , , , , , , , , , ; cwl:out , , , , , , ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cohort_name)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source ; cwl:valueFrom "base-$(self.label)" . rdfs:comment "Maximum distance of variants to consider for merging" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:int . cwl:valueFrom "ALL_READS" . sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "merge" ) ; 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/bcftools-cwl:1.9" ] . sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . sld:type xsd:boolean , sld:null . rdfs:comment "Reference used to generate the alignments" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type , . sld:type xsd:boolean . sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default 1 . cwl:default "Consequence" , "Feature" , "SYMBOL" , "HGVSp" , "HGVSc" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).WgsMetrics.txt" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type xsd:int . sld:type cwl:File , sld:null . cwl:default "$(inputs.input_file.basename).commented.gz" ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_blocklist_bedpe.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_blocklist_bedpe.sh" ) ; 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/basespace_chromoseq:v12" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nset -o errexit\n\nif [[ \"$#\" == 4 ]];then # blocklist_bedpe is passed.\n INPUT_VCF=\"$1\"\n BL_BEDPE=\"$2\"\n SLOPE=\"$3\"\n OUT_BASE=\"$4\"\n\n #CNVkit outputs invalid format like CIPOS=.,894;CIEND=.,894, which can cause svtools vcftobedpe fail\n if [[ \"$INPUT_VCF\" =~ \\.vcf\\.gz$ ]]; then\n /bin/zcat \"$INPUT_VCF\" | /bin/sed -E 's/CIPOS=\\.,[0-9]+;CIEND=\\.,[0-9]+/CIPOS=0,0;CIEND=0,0/g' > fixed_input.vcf\n else\n /bin/sed -E 's/CIPOS=\\.,[0-9]+;CIEND=\\.,[0-9]+/CIPOS=0,0;CIEND=0,0/g' \"$INPUT_VCF\" > fixed_input.vcf\n fi\n #svtools vcftobedpe can take either .vcf or .vcf.gz\n /opt/conda/envs/python2/bin/svtools vcftobedpe -i fixed_input.vcf -o tmp.bedpe\n /bin/grep '^#' tmp.bedpe > tmp.header\n /usr/local/bin/bedtools pairtopair -is -slop \"$SLOPE\" -type notboth -a tmp.bedpe -b \"$BL_BEDPE\" | /bin/cat tmp.header /dev/stdin | /opt/conda/envs/python2/bin/svtools bedpetovcf -i /dev/stdin | /opt/conda/envs/python2/bin/svtools vcfsort /dev/stdin > \"$OUT_BASE.vcf\"\n\n /opt/htslib/bin/bgzip $OUT_BASE.vcf\n /usr/local/bin/tabix -p vcf $OUT_BASE.vcf.gz\nelse # blocklist_bedpe is not passed.\n INPUT_VCF=\"$1\"\n SLOPE=\"$2\"\n OUT_BASE=\"$3\"\n\n /usr/local/bin/bedtools sort -header -i \"$INPUT_VCF\" > $OUT_BASE.vcf\n /opt/htslib/bin/bgzip $OUT_BASE.vcf\n /usr/local/bin/tabix -p vcf $OUT_BASE.vcf.gz\nfi\n" ; cwl:entryname "filter_sv_vcf_blocklist_bedpe.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/basespace_chromoseq:v12" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nset -o errexit\n\nif [[ \"$#\" == 4 ]];then # blocklist_bedpe is passed.\n INPUT_VCF=\"$1\"\n BL_BEDPE=\"$2\"\n SLOPE=\"$3\"\n OUT_BASE=\"$4\"\n\n #CNVkit outputs invalid format like CIPOS=.,894;CIEND=.,894, which can cause svtools vcftobedpe fail\n if [[ \"$INPUT_VCF\" =~ \\.vcf\\.gz$ ]]; then\n /bin/zcat \"$INPUT_VCF\" | /bin/sed -E 's/CIPOS=\\.,[0-9]+;CIEND=\\.,[0-9]+/CIPOS=0,0;CIEND=0,0/g' > fixed_input.vcf\n else\n /bin/sed -E 's/CIPOS=\\.,[0-9]+;CIEND=\\.,[0-9]+/CIPOS=0,0;CIEND=0,0/g' \"$INPUT_VCF\" > fixed_input.vcf\n fi\n #svtools vcftobedpe can take either .vcf or .vcf.gz\n /opt/conda/envs/python2/bin/svtools vcftobedpe -i fixed_input.vcf -o tmp.bedpe\n /bin/grep '^#' tmp.bedpe > tmp.header\n /usr/local/bin/bedtools pairtopair -is -slop \"$SLOPE\" -type notboth -a tmp.bedpe -b \"$BL_BEDPE\" | /bin/cat tmp.header /dev/stdin | /opt/conda/envs/python2/bin/svtools bedpetovcf -i /dev/stdin | /opt/conda/envs/python2/bin/svtools vcfsort /dev/stdin > \"$OUT_BASE.vcf\"\n\n /opt/htslib/bin/bgzip $OUT_BASE.vcf\n /usr/local/bin/tabix -p vcf $OUT_BASE.vcf.gz\nelse # blocklist_bedpe is not passed.\n INPUT_VCF=\"$1\"\n SLOPE=\"$2\"\n OUT_BASE=\"$3\"\n\n /usr/local/bin/bedtools sort -header -i \"$INPUT_VCF\" > $OUT_BASE.vcf\n /opt/htslib/bin/bgzip $OUT_BASE.vcf\n /usr/local/bin/tabix -p vcf $OUT_BASE.vcf.gz\nfi\n" ; cwl:entryname "filter_sv_vcf_blocklist_bedpe.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] . rdfs:comment "output vcf file name" ; cwl:default "duphold_annotated.vcf" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--output" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--output" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File , sld:null . sld:type sld:null ; sld:type [ sld:symbols , , , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:label "Convert default cnvkit .cns output to standard vcf format" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -1 ; CommandLineBinding:prefix "-y" ; cwl:valueFrom "$(inputs.male_reference)" ] "-o" "adjusted.tumor.cns" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "&&" ] "/usr/bin/python" "/usr/local/bin/cnvkit.py" "export" "vcf" "adjusted.tumor.cns" ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/local/bin/cnvkit.py" "call" ) ; 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 "etal/cnvkit:0.9.5" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Coding Variant filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.coding_variant_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.coding_variant_filtered.vcf" ] "--ontology" "--filter" "Consequence is coding_sequence_variant" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . rdfs:comment "number of chromosomes per sample" ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "-ploidy" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type . cwl:default "cnvkit.vcf" ; sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "filters to apply to reads before analysis" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--read_filter" ] ; sld:type xsd:string , sld:null . rdfs:comment "an optional string to prepend to the output filename" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:label "File to be used for annotation, include index file" ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "number of alternate paired reads support needed to pass" ; cwl:default 2 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; sld:type cwl:Directory , xsd:string . 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:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Regions of accessible sequence on chromosomes (.bed), as output by the 'access' command" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--access" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Use or assume a male reference (i.e. female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX)" ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--male-reference" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:boolean . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "source caller of the vcf input file" ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . rdfs:label "Use this annotation for gnomad filtering?" ; sld:type xsd:boolean , sld:null . rdfs:comment "method for size filtering" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/tumorSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--filtering_frequency" ] ; sld:type xsd:double , sld:null . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source ; cwl:valueFrom "##disclaimer=$(self)" . 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" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . sld:type xsd:int . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type xsd:int , sld:null . rdfs:label "a file with a label" ; sld:fields , ; sld:type sld:record . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; sld:type xsd:boolean . cwl:in , , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "#$(self)" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "final" ; sld:type xsd:string , sld:null . rdfs:comment "Minimum base quality for a base to contribute coverage. (N bases are considered to have negative infinite quality and will be excluded regardless of this value.)" ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Create an ideogram of copy ratios on chromosomes as a PDF" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--diagram" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".antitargetcoverage.cnn\";\n if (inputs.normal_bam) {\n glob_base = inputs.normal_bam.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "--normalBam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . sld:type xsd:int . sld:type xsd:string . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--dbsnp" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "Ensembl Variant Effect Predictor" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.vcf.nameroot)_annotated.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v2" ] . rdfs:comment "method used to merge allow multiallelic indels/snps" ; cwl:default "none" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--merge" ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] . cwl:source . cwl:source . sld:type xsd:int , sld:null . cwl:source ; cwl:valueFrom "${ var prefix = self !== null ? self : \"\"; if (inputs.intervals.length == 1 && inputs.intervals[0].match(/^[0-9A-Za-z]+$/)) { return prefix + inputs.intervals[0] + \".g.vcf.gz\"; } else { return prefix + \"output.g.vcf.gz\"; } }" . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type xsd:double , sld:null . sld:type xsd:boolean , sld:null . cwl:in , , , ; cwl:out ; cwl:run . sld:type sld:null ; sld:type [ rdfs:label "custom type, check types directory for input format" ; cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\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 ] . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).GcBiasMetricsSummary.txt" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Picard MergeVcfs" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; 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 40000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:in ; cwl:out ; cwl:run . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type , sld:null . rdfs:comment "Require merged SVs to be on the same strand" ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "${\n if(inputs.same_strand){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . cwl:source . sld:type xsd:int . rdfs:comment "sequence represents the sequencing data as either FASTQs or BAMs with accompanying\nreadgroup information. Note that in the @RG field ID and SM are required.\n" ; rdfs:label "sequence: sequencing data and readgroup information" ; sld:type [ sld:items ; sld:type sld:array ] . rdfs:comment "Previously generated reference.cnn file" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--reference" ] ; sld:type cwl:File . cwl:source . cwl:default "manta" . cwl:source . rdfs:label "Used as key for new VEP annotation" ; sld:type xsd:string . rdfs:comment "Fasta file with adapters for removal that may contain N." ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:in , , , , , ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . sld:fields ; sld:type sld:record . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in , , , , ; cwl:out , , , , ; cwl:run . cwl:source . rdfs:comment "BAM or CRAM input" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:default "out" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:default "v" . a cwl:CommandLineTool ; rdfs:label "samtools index cram" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/local/bin/samtools" "index" "$(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 ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.cram; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputSource ; sld:type cwl:File . cwl:default "Workflow source can be found at https://github.com/genome/analysis-workflows" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "vcf index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/local/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 ; 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 ; 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 ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; 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 "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; 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 "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] . 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: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 ; 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 ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; 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: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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "set" , "REF" , "POS" , "CHROM" , "ALT" , "ID" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:default "none" . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot)-scatter.pdf" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type xsd:int , sld:null . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; sld:type cwl:File . cwl:source . sld:type cwl:Directory , xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; sld:type cwl:File . 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 . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . a cwl:Workflow ; rdfs:label "exome alignment and germline 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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . sld:type xsd:string , sld:null . cwl:in ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).GcBiasMetrics.txt" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "apply BQSR" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_name).bam" ] "--static-quantized-quals" "10" "--static-quantized-quals" "20" "--static-quantized-quals" "30" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "ApplyBQSR" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . rdfs:comment "size in bp used for filtering" ; cwl:default 50000 ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int , sld:null . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:source . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . sld:type xsd:int . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . rdfs:comment "output vcf file name" ; cwl:default "filtered_sv.vcf" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . sld:type xsd:double , sld:null . cwl:default "MarkedSorted.bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . cwl:default "SURVIVOR-merged-AnnotSV.tsv" . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default "0.05" . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int . cwl:source . a cwl:CommandLineTool ; rdfs:label "samtools index" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/local/bin/samtools" "index" "$(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:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source ; cwl:valueFrom "$(self.readgroup)" . 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:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:fields , ; sld:type sld:record . cwl:default "filtered_cnvkit.vcf" . cwl:default "chr4" , "chr14" , "chr11" , "chr16" , "chr2" , "chr7" , "chr5" , "chr12" , "chr17" , "chr19" , "chr22" , "chr20" , "chr8" , "chr1" , "chr3" , "chr13" , "chr10" , "chr18" , "chr15" , "chr21" , "chr6" , "chr9" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:default "final" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "INTERVALS=" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . rdfs:comment "resolve duplicate sample names" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--force-samples" ] ; sld:type xsd:boolean , sld:null . cwl:source ; cwl:valueFrom "#$(self)" . rdfs:comment "snps vcf file to annotate hom/het variant counts within sv" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--snp" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--snp" ] ; sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; sld:type cwl:File , xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "create BQSR table" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/bqsr.table" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "BaseRecalibrator" ) ; 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 "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . sld:type , sld:null . cwl:in , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "annotated.coding_variant_filtered.vcf" ] ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . rdfs:comment "sequence represents the sequencing data as either FASTQs or BAMs with accompanying\nreadgroup information. Note that in the @RG field ID and SM are required.\n" ; rdfs:label "sequence: sequencing data and readgroup information" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Note: cnvkit batch is a complex command that is capable of running all or part of the cnvkit internal\npipeline, depending on the combination of inputs provided to it. In order to take advantage of this,\nmost inputs to this cwl are optional, so that different workflows can use different forms of the\ncommand while still using a single cwl file. For further reading, see the relevant cnvkit docs at\nhttps://cnvkit.readthedocs.io/en/stable/quickstart.html#build-a-reference-from-normal-samples-and-infer-tumor-copy-ratios\nhttps://cnvkit.readthedocs.io/en/stable/pipeline.html#batch\nIn our pipelines, the command form is mainly determined by the components of the reference input. The\nsomatic_exome cwl pipeline provides a fasta file and a normal bam, which causes the batch pipeline to\nconstruct a copy number reference (.cnn file) based on the normal bam. The germline_wgs cwl pipeline\ndoes not provide a normal bam; instead it passes a cnn reference file as an optional input. This file\nis intended to be manually generated from a reference normal sample for use in the pipeline. If it is\nnot provided, cnvkit will automatically generate a flat reference file.\n" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$((inputs.reference.hasOwnProperty('cnn_file'))? null : '--normal')" ] ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/local/bin/cnvkit.py" "batch" ) ; cwl:cwlVersion ; 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:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "etal/cnvkit:0.9.5" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . sld:type cwl:File . cwl:source , ; cwl:valueFrom "${\n var cnn = self[0];\n var fasta = self[1];\n return {'cnn_file': cnn, 'fasta_file': fasta};\n}\n" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:double , sld:null . cwl:default 1 ; 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 . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type [ cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--known-sites" ] ; sld:items cwl:File ; sld:type sld:array ] . rdfs:label "Identify known variants colocated with input variant" ; sld:type xsd:boolean . 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; 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:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--tumorBam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "add VEP annotation to report" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; 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 "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:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot)-diagram.pdf" ] ; sld:type cwl:File , sld:null . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . cwl:in , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-contamination" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).CNVnator.cn" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:default 2 . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).bw" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--targets" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . rdfs:comment "output file name" ; cwl:default "AnnotSV.tsv" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-outputFile" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-outputFile" ] ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this" ; rdfs:label "align with bwa_mem and tag" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-n" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/bin/bash" "sequence_alignment_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\nset -o nounset\n\nRUN_TRIMMING=\"false\"\n\nwhile getopts \"b:?1:?2:?g:r:n:t:?o:?\" 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=\"$OPTARG\"\n ;;\n t)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTERS=\"$OPTARG\"\n ;;\n o)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTER_MIN_OVERLAP=\"$OPTARG\"\n ;;\n esac\ndone\n\nif [[ \"$MODE\" == 'fastq' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -R \"$READGROUP\" \"$REFERENCE\" \"$FASTQ1\" \"$FASTQ2\" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads \"$FASTQ1\" --reads2 \"$FASTQ2\" --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\nif [[ \"$MODE\" == 'bam' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout \\\n | /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads - --interleaved --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\n" ; cwl:entryname "sequence_alignment_helper.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:stdout "refAlign.bam" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--fasta" ] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-2" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; sld:type cwl:File , sld:null . cwl:default "cn" . rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--assembly" ] ; sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.file)" . a cwl:Workflow ; rdfs:label "Subworkflow that runs cnvkit in single sample mode and returns a 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:StepInputExpressionRequirement ] . cwl:default 1 . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:default "queryname" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . sld:type xsd:boolean , sld:null . rdfs:comment "input bgzipped tabix indexed vcfs to merge" ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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:outputSource ; sld:type cwl:File . 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 . sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ cwl:valueFrom "$( ['-t', self.adapters.path, '-o', self.min_overlap] )" ] ; sld:type , sld:null . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).targetcoverage.cnn" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Minimum overlap for removal without pair overlap." ; sld:type xsd:int . cwl:default "ALL_READS" ; sld:type xsd:string . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . rdfs:comment "Drop very-low-coverage bins before segmentation to avoid false-positive deletions in poor-quality tumor samples" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--drop-low-coverage" ] ; sld:type xsd:boolean , sld:null . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File , sld:null . sld:type xsd:boolean , sld:null . cwl:valueFrom "annotated.filtered.vcf" . rdfs:comment "slope(bp) used in bedtools pairtopair" ; cwl:default 100 ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int , sld:null . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf" ] ; sld:type cwl:File . cwl:default "AD" , "AF" , "DP" , "GT" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:default "SURVIVOR-sv-merged.vcf" . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "bcftools-merged-AnnotSV.tsv" . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ; sld:type xsd:string . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_tsv_name)" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Sambamba: merge" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-t" "$(runtime.cores)" ) ; cwl:baseCommand ( "/bin/bash" "merge.sh" ) ; 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 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam-merge:0.1" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -o pipefail\nset -o errexit\nset -o nounset\n\nSORTED=false\n\nwhile getopts \"t:n:s:\" opt; do\n case \"$opt\" in\n t)\n NTHREADS=\"$OPTARG\"\n ;;\n n)\n OUTFILENAME=\"$OPTARG\"\n ;;\n s)\n SORTED=true\n ;;\n esac\ndone\n\nBAMS=(\"${@:$OPTIND}\")\nNUM_BAMS=${#BAMS[@]}\n\n#if there is only one bam, just copy it and index it\nif [[ $NUM_BAMS -eq 1 ]]; then\n cp \"$BAMS\" \"$OUTFILENAME\";\nelse\n if [[ $SORTED == \"true\" ]];then\n /usr/bin/sambamba merge -t \"$NTHREADS\" \"$OUTFILENAME\" \"${BAMS[@]}\"\n else #unsorted bams, use picard\n args=(OUTPUT=\"$OUTFILENAME\" ASSUME_SORTED=true USE_THREADING=true SORT_ORDER=unsorted VALIDATION_STRINGENCY=LENIENT)\n for i in \"${BAMS[@]}\";do\n args+=(\"INPUT=$i\")\n done\n java -jar -Xmx6g /opt/picard/picard.jar MergeSamFiles \"${args[@]}\"\n fi\nfi\nif [[ $SORTED == \"true\" ]];then\n /usr/bin/sambamba index \"$OUTFILENAME\"\nfi\n" ; cwl:entryname "merge.sh" ] ] . rdfs:comment "Minimum mapping quality for a read to contribute coverage." ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-genomeBuild" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-genomeBuild" ] ; sld:type xsd:string . rdfs:comment "source caller of the vcf input file" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; 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:in , , , , , , , , , , ; cwl:out ; cwl:run . sld:type xsd:boolean . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default "Frameshift" , "Wildtype" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:double , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:default false . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . rdfs:comment "List of chromosomes to run CNVnator on" ; cwl:default "chr6" , "chr12" , "chr1" , "chr21" , "chr19" , "chr4" , "chr9" , "chr2" , "chr22" , "chr10" , "chrX" , "chr17" , "chr7" , "chrY" , "chr18" , "chr20" , "chr15" , "chr8" , "chr16" , "chr5" , "chr13" , "chr14" , "chr3" , "chr11" ; cwl:inputBinding [ CommandLineBinding:itemSeparator " " ; CommandLineBinding:position 3 ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--everything" ] ; sld:type xsd:boolean , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:default "filtered_manta.vcf" . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:default "merged" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:default 1 . cwl:source . cwl:source ; cwl:valueFrom "#$(self)" . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . sld:type xsd:double , sld:null . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:source . cwl:source . rdfs:comment "Create a whole-genome copy ratio profile as a PDF scatter plot" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--scatter" ] ; sld:type xsd:boolean , sld:null . a cwl:ExpressionTool ; ExpressionTool:expression "${\n var metrics = inputs.verify_bam_id_metrics.contents.split(\"\\n\");\n if ( metrics[0].split(\"\\t\")[6] == 'FREEMIX' ) {\n return {'freemix_score': metrics[1].split(\"\\t\")[6]};\n } else {\n return {'freemix_score:': null };\n }\n}\n" ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . 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 [] ; sld:type xsd:string , cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:default "select_variants" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_read_support.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_read_support.sh" ) ; 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 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nabundance=\"$1\"\ninput_vcf=\"$2\"\noutput_vcf=\"$3\"\npaired_count=\"$4\"\nsplit_count=\"$5\"\nvcf_source=\"$6\"\n\nif [ \"$vcf_source\" == \"smoove\" ]; then\n echo \"Running filter for smoove vcf\"\n filter_expression=\"((AS >= $split_count) && (AP >= $paired_count) && ((AP+AS) / (AP+RP+AS+RS) >= $abundance))\"\nelif [ \"$vcf_source\" == \"manta\" ]; then\n echo \"Running filter for manta vcf\"\n filter_expression=\"((SR[0:*]=\\\".\\\" || (SR[0:1] >= $split_count)) && (PR[0:1] >= $paired_count) && ((SR[0:*]=\\\".\\\" && (PR[0:1] / (PR[0:0]+PR[0:1]) >= $abundance))|| ((SR[0:1]+PR[0:1]) / (SR[0:0]+SR[0:1]+PR[0:1]+PR[0:0]) >= $abundance)))\"\nelse\n echo \"vcf source: '$vcf_source' is not supported for SV filtering\"\n exit 1\nfi\n\n/opt/bcftools/bin/bcftools filter \"$input_vcf\" -o \"$output_vcf\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_read_support.sh" ] ] ; 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\n\nabundance=\"$1\"\ninput_vcf=\"$2\"\noutput_vcf=\"$3\"\npaired_count=\"$4\"\nsplit_count=\"$5\"\nvcf_source=\"$6\"\n\nif [ \"$vcf_source\" == \"smoove\" ]; then\n echo \"Running filter for smoove vcf\"\n filter_expression=\"((AS >= $split_count) && (AP >= $paired_count) && ((AP+AS) / (AP+RP+AS+RS) >= $abundance))\"\nelif [ \"$vcf_source\" == \"manta\" ]; then\n echo \"Running filter for manta vcf\"\n filter_expression=\"((SR[0:*]=\\\".\\\" || (SR[0:1] >= $split_count)) && (PR[0:1] >= $paired_count) && ((SR[0:*]=\\\".\\\" && (PR[0:1] / (PR[0:0]+PR[0:1]) >= $abundance))|| ((SR[0:1]+PR[0:1]) / (SR[0:0]+SR[0:1]+PR[0:1]+PR[0:0]) >= $abundance)))\"\nelse\n echo \"vcf source: '$vcf_source' is not supported for SV filtering\"\n exit 1\nfi\n\n/opt/bcftools/bin/bcftools filter \"$input_vcf\" -o \"$output_vcf\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_read_support.sh" ] ] . cwl:outputBinding [ CommandOutputBinding:glob "${ \n var glob_base = \".antitarget.bed\";\n if (inputs.bait_intervals) {\n glob_base = inputs.bait_intervals.nameroot + glob_base;\n } \n return glob_base;\n} \n" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source ; cwl:valueFrom "#$(self)" . a cwl:CommandLineTool ; rdfs:label "collect alignment summary metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "OUTPUT=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:default "duphold" . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory , xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf_summary.html" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect WGS metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).WgsMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectWgsMetrics" ) ; 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 "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:default true . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:boolean , sld:null . sld:type xsd:boolean . cwl:source . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 4.1.8.1)" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "VariantsToTable" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "VariantsToTable" ) ; 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: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 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:in , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "collect insert size metrics" ; ns1:original_cwlVersion "v1.0" ; 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: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 18000 ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type xsd:double , sld:null . rdfs:comment "blocklist bedpe file" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File , sld:null . cwl:default 1 . cwl:outputSource ; sld:type cwl:File . rdfs:label "custom annotation file to be used by vep" ; sld:fields , , ; sld:type sld:record . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source .