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SNPs in these files will be ignored unless the --mismatchFraction argument is used. optional parameter.", "id": "#GATK-BaseRecalibrator.cwl/knownSites" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--list" }, "doc": "List the available covariates and exit", "id": "#GATK-BaseRecalibrator.cwl/list" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--lowMemoryMode" }, "doc": "Reduce memory usage in multi-threaded code at the expense of threading efficiency", "id": "#GATK-BaseRecalibrator.cwl/lowMemoryMode" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--low_quality_tail" }, "doc": "minimum quality for the bases in the tail of the reads to be considered", "id": "#GATK-BaseRecalibrator.cwl/low_quality_tail" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--maximum_cycle_value" }, "doc": "The maximum cycle value permitted for the Cycle covariate", "id": "#GATK-BaseRecalibrator.cwl/maximum_cycle_value" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--mismatches_context_size" }, "doc": "Size of the k-mer context to be used for base mismatches", "id": "#GATK-BaseRecalibrator.cwl/mismatches_context_size" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--mismatches_default_quality" }, "doc": "default quality for the base mismatches covariate", "id": "#GATK-BaseRecalibrator.cwl/mismatches_default_quality" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--no_standard_covs" }, "doc": "Do not use the standard set of covariates, but rather just the ones listed using the -cov argument", "id": "#GATK-BaseRecalibrator.cwl/no_standard_covs" }, { "type": [ "null", "File" ], "inputBinding": { "position": 2, "prefix": "--out" }, "doc": "The output recalibration table file to create", "id": "#GATK-BaseRecalibrator.cwl/out" }, { "type": "string", "inputBinding": { "position": 2, "prefix": "-o" }, "doc": "name of the output file from baseRecalibrator", "id": "#GATK-BaseRecalibrator.cwl/outputfile_BaseRecalibrator" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--quantizing_levels" }, "doc": "Sort the rows in the tables of reports. Whether GATK report tables should have rows in sorted order, starting from leftmost column", "id": "#GATK-BaseRecalibrator.cwl/quantizing_levels" }, { "type": "File", "inputBinding": { "position": 2, "prefix": "-R" }, "secondaryFiles": [ ".amb", ".ann", ".bwt", ".pac", ".sa", ".fai", "^.dict" ], "id": "#GATK-BaseRecalibrator.cwl/reference" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--run_without_dbsnp_potentially_ruining_quality" }, "doc": "If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.", "id": "#GATK-BaseRecalibrator.cwl/run_without_dbsnp_potentially_ruining_quality" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--solid_nocall_strategy" }, "doc": "Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ", "id": "#GATK-BaseRecalibrator.cwl/solid_nocall_strategy" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--solid_recal_mode" }, "doc": "How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS", "id": "#GATK-BaseRecalibrator.cwl/solid_recal_mode" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--sort_by_all_columns" }, "doc": "Sort the rows in the tables of reports. Whether GATK report tables should have rows in sorted order, starting from leftmost column", "id": "#GATK-BaseRecalibrator.cwl/sort_by_all_columns" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.outputfile_BaseRecalibrator)" }, "id": "#GATK-BaseRecalibrator.cwl/output_baseRecalibrator" } ], "arguments": [ { "valueFrom": "$(runtime.tmpdir)", "position": 0, "separate": false, "prefix": "-Djava.io.tmpdir=" }, { "valueFrom": "BaseRecalibrator", "position": 2, "prefix": "-T" } ], "baseCommand": [ "java" ], "doc": "GATK-BaseRecalibrator.cwl is developed for CWL consortium\nIt generate base recalibration table to compensate for systematic errors in basecalling confidences\n Usage: java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I my_reads.bam -knownSites latest_dbsnp.vcf -o recal_data.table.\n", "id": "#GATK-BaseRecalibrator.cwl" }, { "class": "CommandLineTool", "requirements": [ { "$import": "#envvar-global.yml" }, { "class": "DockerRequirement", "dockerPull": "dukegcb/gatk-base:3" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "3.8" ], "package": "gatk", "https://schema.org/citation": "https://dx.doi.org/10.1038/ng.806" } ] } ], "inputs": [ { "type": "File", "inputBinding": { "position": 1, "prefix": "-jar" }, "id": "#GATK-GenotypeGVCFs.cwl/GATKJar" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--annotateNDA" }, "doc": "If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site", "id": "#GATK-GenotypeGVCFs.cwl/annotateNDA" }, { "type": [ "null", { "type": "array", "items": "string" } ], "inputBinding": { "position": 2, "prefix": "--annotation" }, "doc": "One or more specific annotations to apply to variant calls", "id": "#GATK-GenotypeGVCFs.cwl/annotation" }, { "type": [ "null", "File" ], "inputBinding": { "position": 2, "prefix": "--dbsnp" }, "doc": "latest_dbsnp.vcf set of known indels", "id": "#GATK-GenotypeGVCFs.cwl/dbsnp" }, { "type": [ "null", { "type": "array", "items": "string" } ], "inputBinding": { "position": 2, "prefix": "--group" }, "doc": "One or more classes/groups of annotations to apply to variant calls", "id": "#GATK-GenotypeGVCFs.cwl/group" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--heterozygosity" }, "doc": "Heterozygosity for indel calling", "id": "#GATK-GenotypeGVCFs.cwl/heterozygosity" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--heterozygosity_stdev" }, "doc": "Heterozygosity for indel calling", "id": "#GATK-GenotypeGVCFs.cwl/heterozygosity_stdev" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--includeNonVariantSites" }, "doc": "Include loci found to be non-variant after genotyping", "id": "#GATK-GenotypeGVCFs.cwl/includeNonVariantSites" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--indel_heterozygosity" }, "doc": "Heterozygosity for indel calling", "id": "#GATK-GenotypeGVCFs.cwl/indel_heterozygosity" }, { "type": [ "null", { "type": "array", "items": "double" } ], "inputBinding": { "position": 2, "prefix": "--input_prior" }, "doc": "Input prior for calls", "id": "#GATK-GenotypeGVCFs.cwl/input_prior" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--interval_padding" }, "doc": "Amount of padding (in bp) to add to each interval", "id": "#GATK-GenotypeGVCFs.cwl/interval_padding" }, { "type": [ "null", { "type": "array", "items": "File" } ], "inputBinding": { "position": 2, "prefix": "--intervals" }, "doc": "One or more genomic intervals over which to operate", "id": "#GATK-GenotypeGVCFs.cwl/intervals" }, { "type": "string", "default": "-Xmx4g", "inputBinding": { "position": 0 }, "id": "#GATK-GenotypeGVCFs.cwl/java_arg" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--max_alternate_alleles" }, "doc": "Maximum number of alternate alleles to genotype", "id": "#GATK-GenotypeGVCFs.cwl/max_alternate_alleles" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--max_genotype_count" }, "doc": "Maximum number of genotypes to consider at any site", "id": "#GATK-GenotypeGVCFs.cwl/max_genotype_count" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--max_num_PL_values" }, "doc": "Maximum number of PL values to output", "id": "#GATK-GenotypeGVCFs.cwl/max_num_PL_values" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "-o" }, "doc": "name of the output file from GenotypeGVCFs", "id": "#GATK-GenotypeGVCFs.cwl/outputfile_GenotypeGVCFs" }, { "type": "File", "inputBinding": { "position": 2, "prefix": "-R" }, "secondaryFiles": [ ".amb", ".ann", ".bwt", ".pac", ".sa", ".fai", "^.dict" ], "doc": "Reference genome assembly, indexed", "id": "#GATK-GenotypeGVCFs.cwl/reference" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--sample_ploidy" }, "doc": "Use additional trigger on variants found in an external alleles file", "id": "#GATK-GenotypeGVCFs.cwl/sample_ploidy" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--standard_min_confidence_threshold_for_calling" }, "doc": "The minimum phred-scaled confidence threshold at which variants should be called", "id": "#GATK-GenotypeGVCFs.cwl/stand_call_conf" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "-nt" }, "doc": "Number of data threads to allocate to this analysis", "id": "#GATK-GenotypeGVCFs.cwl/threads" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--useNewAFCalculator" }, "doc": "Use new AF model instead of the so-called exact model", "id": "#GATK-GenotypeGVCFs.cwl/useNewAFCalculator" }, { "type": { "type": "array", "items": "File", "inputBinding": { "prefix": "-V" } }, "inputBinding": { "position": 2 }, "doc": "One or more input gVCF files", "id": "#GATK-GenotypeGVCFs.cwl/variants" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.outputfile_GenotypeGVCFs)" }, "secondaryFiles": [ ".idx" ], "id": "#GATK-GenotypeGVCFs.cwl/output_GenotypeGVCFs" } ], "arguments": [ { "valueFrom": "$(runtime.tmpdir)", "position": 0, "separate": false, "prefix": "-Djava.io.tmpdir=" }, { "valueFrom": "GenotypeGVCFs", "position": 2, "prefix": "-T" } ], "baseCommand": [ "java" ], "doc": "GATK-GenotypeGVCFs.cwl is developed for CWL consortium\nPerform joint genotyping on gVCF files produced by HaplotypeCaller\n", "id": "#GATK-GenotypeGVCFs.cwl" }, { "class": "CommandLineTool", "requirements": [ { "$import": "#envvar-global.yml" }, { "class": "DockerRequirement", "dockerPull": "dukegcb/gatk-base:3" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "3.8" ], "package": "gatk", "https://schema.org/citation": "https://dx.doi.org/10.1038/ng.806" } ] } ], "inputs": [ { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--indelSizeToEliminateInRefModel" }, "doc": "The size of an indel to check for in the reference model", "id": "#GATK-HaplotypeCaller.cwl/ERCIS" }, { "type": "File", "inputBinding": { "position": 1, "prefix": "-jar" }, "id": "#GATK-HaplotypeCaller.cwl/GATKJar" }, { "type": [ "null", { "type": "array", "items": "int" } ], "inputBinding": { "position": 2 }, "doc": "Input prior for calls", "id": "#GATK-HaplotypeCaller.cwl/GVCFGQBands" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--activeProbabilityThreshold" }, "doc": "Threshold for the probability of a profile state being active.", "id": "#GATK-HaplotypeCaller.cwl/activeProbabilityThreshold" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--activeRegionExtension" }, "doc": "The active region extension; if not provided defaults to Walker annotated default", "id": "#GATK-HaplotypeCaller.cwl/activeRegionExtension" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--activeRegionMaxSize" }, "doc": "The active region maximum size; if not provided defaults to Walker annotated default", "id": "#GATK-HaplotypeCaller.cwl/activeRegionMaxSize" }, { "type": [ "null", "File" ], "inputBinding": { "position": 2, "prefix": "--activeRegionOut" }, "doc": "Output the active region to this IGV formatted file", "id": "#GATK-HaplotypeCaller.cwl/activeRegionOut" }, { "type": [ "null", "File" ], "inputBinding": { "position": 2, "prefix": "--activityProfileOut" }, "doc": "Output the raw activity profile results in IGV format", "id": "#GATK-HaplotypeCaller.cwl/activityProfileOut" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--allSitePLs" }, "doc": "Annotate all sites with PLs", "id": "#GATK-HaplotypeCaller.cwl/allSitePLs" }, { "type": [ "null", { "type": "array", "items": "string" } ], "inputBinding": { "position": 2 }, "doc": "The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES", "id": "#GATK-HaplotypeCaller.cwl/alleles" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--allowNonUniqueKmersInRef" }, "doc": "Allow graphs that have non-unique kmers in the reference", "id": "#GATK-HaplotypeCaller.cwl/allowNonUniqueKmersInRef" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--annotateNDA" }, "doc": "If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site", "id": "#GATK-HaplotypeCaller.cwl/annotateNDA" }, { "type": [ "null", { "type": "array", "items": "string" } ], "inputBinding": { "position": 2 }, "doc": "One or more specific annotations to apply to variant calls", "id": "#GATK-HaplotypeCaller.cwl/annotation" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--bamOutput" }, "doc": "File to which assembled haplotypes should be written", "id": "#GATK-HaplotypeCaller.cwl/bamOutput" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--bamWriterType" }, "doc": "Which haplotypes should be written to the BAM.", "id": "#GATK-HaplotypeCaller.cwl/bamWriterType" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--consensus" }, "doc": "The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default", "id": "#GATK-HaplotypeCaller.cwl/bandPassSigma" }, { "type": [ "null", { "type": "array", "items": "string" } ], "inputBinding": { "position": 2 }, "doc": "comp binds reference ordered data. This argument supports ROD files of the following types BCF2, VCF, VCF3", "id": "#GATK-HaplotypeCaller.cwl/comp" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--consensus" }, "doc": "Print out very verbose debug information about each triggering active region", "id": "#GATK-HaplotypeCaller.cwl/consensus" }, { "type": [ "null", "File" ], "inputBinding": { "position": 2, "prefix": "--contamination_fraction_to_filter" }, "doc": "Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be \"\" (Contamination is double) per line; No header.", "id": "#GATK-HaplotypeCaller.cwl/contamination" }, { "type": [ "null", "int" ], "doc": "controls the number of CPU threads allocated to each data thread", "inputBinding": { "position": 2, "prefix": "-nct" }, "id": "#GATK-HaplotypeCaller.cwl/cpu_threads" }, { "type": [ "null", "File" ], "inputBinding": { "position": 2, "prefix": "--dbsnp" }, "doc": "latest_dbsnp.vcf set of known indels", "id": "#GATK-HaplotypeCaller.cwl/dbsnp" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--debug" }, "doc": "Print out very verbose debug information about each triggering active region", "id": "#GATK-HaplotypeCaller.cwl/debug" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--disableOptimizations" }, "doc": "Dont skip calculations in ActiveRegions with no variants", "id": "#GATK-HaplotypeCaller.cwl/disableOptimizations" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--doNotRunPhysicalPhasing" }, "doc": "As of GATK 3.3, HaplotypeCaller outputs physical (read-based) information (see version 3.3 release notes and documentation for details). This argument disables that behavior.", "id": "#GATK-HaplotypeCaller.cwl/doNotRunPhysicalPhasing" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--dontIncreaseKmerSizesForCycles" }, "doc": "Disable iterating over kmer sizes when graph cycles are detected", "id": "#GATK-HaplotypeCaller.cwl/dontIncreaseKmerSizesForCycles" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--dontTrimActiveRegions" }, "doc": "If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping", "id": "#GATK-HaplotypeCaller.cwl/dontTrimActiveRegions" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--emitRefConfidence" }, "doc": "Mode for emitting reference confidence scores", "id": "#GATK-HaplotypeCaller.cwl/emitRefConfidence" }, { "type": [ "null", { "type": "array", "items": "string" } ], "inputBinding": { "position": 2 }, "doc": "One or more specific annotations to exclude", "id": "#GATK-HaplotypeCaller.cwl/excludeAnnotation" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--forceActive" }, "doc": "If provided, all bases will be tagged as active", "id": "#GATK-HaplotypeCaller.cwl/forceActive" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--gcpHMM" }, "doc": "Flat gap continuation penalty for use in the Pair HMM", "id": "#GATK-HaplotypeCaller.cwl/gcpHMM" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--genotyping_mode" }, "doc": "The --genotyping_mode argument is an enumerated type (GenotypingOutputMode), which can have one of the following values", "id": "#GATK-HaplotypeCaller.cwl/genotyping_mode" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--phredScaledGlobalReadMismappingRate" }, "doc": "The global assumed mismapping rate for reads", "id": "#GATK-HaplotypeCaller.cwl/globalMAPQ" }, { "type": [ "null", "File" ], "inputBinding": { "position": 2, "prefix": "--graphOutput" }, "doc": "Write debug assembly graph information to this file", "id": "#GATK-HaplotypeCaller.cwl/graphOutput" }, { "type": { "type": "array", "items": "string", "inputBinding": { "prefix": "--group" } }, "inputBinding": { "position": 2 }, "doc": "One or more classes/groups of annotations to apply to variant calls", "id": "#GATK-HaplotypeCaller.cwl/group" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--heterozygosity" }, "doc": "Heterozygosity for indel calling", "id": "#GATK-HaplotypeCaller.cwl/heterozygosity" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--indel_heterozygosity" }, "doc": "Heterozygosity for indel calling", "id": "#GATK-HaplotypeCaller.cwl/indel_heterozygosity" }, { "type": "File", "inputBinding": { "position": 2, "prefix": "-I" }, "secondaryFiles": [ "^.bai" ], "doc": "bam file produced after printReads", "id": "#GATK-HaplotypeCaller.cwl/inputBam_HaplotypeCaller" }, { "type": [ "null", { "type": "array", "items": "double" } ], "inputBinding": { "position": 2 }, "doc": "Input prior for calls", "id": "#GATK-HaplotypeCaller.cwl/input_prior" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--interval_padding" }, "doc": "Amount of padding (in bp) to add to each interval", "id": "#GATK-HaplotypeCaller.cwl/interval_padding" }, { "type": [ "null", { "type": "array", "items": "File" } ], "inputBinding": { "position": 2, "prefix": "--intervals" }, "doc": "One or more genomic intervals over which to operate", "id": "#GATK-HaplotypeCaller.cwl/intervals" }, { "type": "string", "default": "-Xmx4g", "inputBinding": { "position": 0 }, "id": "#GATK-HaplotypeCaller.cwl/java_arg" }, { "type": [ "null", { "type": "array", "items": "int" } ], "inputBinding": { "position": 2 }, "doc": "Kmer size to use in the read threading assembler", "id": "#GATK-HaplotypeCaller.cwl/kmerSize" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--maxNumHaplotypesInPopulation" }, "doc": "Maximum number of haplotypes to consider for your population", "id": "#GATK-HaplotypeCaller.cwl/maxNumHaplotypesInPopulation" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--maxReadsInRegionPerSample" }, "doc": "Maximum reads in an active region", "id": "#GATK-HaplotypeCaller.cwl/maxReadsInRegionPerSample" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--max_alternate_alleles" }, "doc": "Maximum number of alternate alleles to genotype", "id": "#GATK-HaplotypeCaller.cwl/max_alternate_alleles" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--minDanglingBranchLength" }, "doc": "Minimum length of a dangling branch to attempt recovery", "id": "#GATK-HaplotypeCaller.cwl/minDanglingBranchLength" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--minPruning" }, "doc": "Minimum support to not prune paths in the graph", "id": "#GATK-HaplotypeCaller.cwl/minPruning" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--minReadsPerAlignmentStart" }, "doc": "Minimum number of reads sharing the same alignment start for each genomic location in an active region", "id": "#GATK-HaplotypeCaller.cwl/minReadsPerAlignmentStart" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--min_base_quality_score" }, "doc": "Minimum base quality required to consider a base for calling", "id": "#GATK-HaplotypeCaller.cwl/min_base_quality_score" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--numPruningSamples" }, "doc": "Number of samples that must pass the minPruning threshold", "id": "#GATK-HaplotypeCaller.cwl/numPruningSamples" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--output_mode" }, "doc": "The PCR indel model to use", "id": "#GATK-HaplotypeCaller.cwl/output_mode" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "-o" }, "doc": "name of the output file from HaplotypeCaller", "id": "#GATK-HaplotypeCaller.cwl/outputfile_HaplotypeCaller" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--pcr_indel_model" }, "doc": "The PCR indel model to use", "id": "#GATK-HaplotypeCaller.cwl/pcr_indel_model" }, { "type": "File", "inputBinding": { "position": 2, "prefix": "-R" }, "secondaryFiles": [ ".amb", ".ann", ".bwt", ".pac", ".sa", ".fai", "^.dict" ], "id": "#GATK-HaplotypeCaller.cwl/reference" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--sample_name" }, "doc": "Use additional trigger on variants found in an external alleles file", "id": "#GATK-HaplotypeCaller.cwl/sample_name" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--sample_ploidy" }, "doc": "Use additional trigger on variants found in an external alleles file", "id": "#GATK-HaplotypeCaller.cwl/sample_ploidy" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--standard_min_confidence_threshold_for_calling" }, "doc": "The minimum phred-scaled confidence threshold at which variants should be called", "id": "#GATK-HaplotypeCaller.cwl/stand_call_conf" }, { "type": [ "null", "double" ], "inputBinding": { "position": 2, "prefix": "--standard_min_confidence_threshold_for_emitting" }, "doc": "The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)", "id": "#GATK-HaplotypeCaller.cwl/stand_emit_conf" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--useAllelesTrigger" }, "doc": "Use additional trigger on variants found in an external alleles file", "id": "#GATK-HaplotypeCaller.cwl/useAllelesTrigger" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--useFilteredReadsForAnnotations" }, "doc": "Use the contamination-filtered read maps for the purposes of annotating variants", "id": "#GATK-HaplotypeCaller.cwl/useFilteredReadsForAnnotations" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--variant_index_parameter" }, "doc": "Index parameter, needed by emitRefConfidence GVCF if output extension not .g.vcf", "id": "#GATK-HaplotypeCaller.cwl/variant_index_parameter" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--variant_index_type" }, "doc": "Index type, needed by emitRefConfidence GVCF if output extension not .g.vcf", "id": "#GATK-HaplotypeCaller.cwl/variant_index_type" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.outputfile_HaplotypeCaller)" }, "secondaryFiles": [ ".idx" ], "id": "#GATK-HaplotypeCaller.cwl/output_HaplotypeCaller" }, { "type": [ "null", "File" ], "outputBinding": { "glob": "$(inputs.bamOutput)" }, "id": "#GATK-HaplotypeCaller.cwl/output_HaplotypesBam" } ], "arguments": [ { "valueFrom": "$(runtime.tmpdir)", "position": 0, "separate": false, "prefix": "-Djava.io.tmpdir=" }, { "valueFrom": "HaplotypeCaller", "position": 2, "prefix": "-T" } ], "baseCommand": [ "java" ], "doc": "GATK-RealignTargetCreator.cwl is developed for CWL consortium\nCall germline SNPs and indels via local re-assembly of haplotypes\n", "id": "#GATK-HaplotypeCaller.cwl" }, { "class": "CommandLineTool", "requirements": [ { "$import": "#envvar-global.yml" }, { "class": "DockerRequirement", "dockerPull": "dukegcb/gatk-base:3" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "3.8" ], "package": "gatk", "https://schema.org/citation": "https://dx.doi.org/10.1038/ng.806" } ] } ], "inputs": [ { "type": "File", "inputBinding": { "position": 1, "prefix": "-jar" }, "id": "#GATK-PrintReads.cwl/GATKJar" }, { "type": [ "null", "int" ], "doc": "controls the number of CPU threads allocated to each data thread", "default": 8, "inputBinding": { "position": 2, "prefix": "-nct" }, "id": "#GATK-PrintReads.cwl/cpu_threads" }, { "type": "File", "inputBinding": { "position": 2, "prefix": "-I" }, "secondaryFiles": [ "^.bai" ], "doc": "bam file produced after indelRealigner", "id": "#GATK-PrintReads.cwl/inputBam_printReads" }, { "type": "File", "inputBinding": { "position": 2, "prefix": "-BQSR" }, "doc": "the recalibration table produced by BaseRecalibration", "id": "#GATK-PrintReads.cwl/input_baseRecalibrator" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--interval_padding" }, "doc": "Amount of padding (in bp) to add to each interval", "id": "#GATK-PrintReads.cwl/interval_padding" }, { "type": [ "null", { "type": "array", "items": "File", "inputBinding": { "prefix": "--intervals" } } ], "inputBinding": { "position": 2 }, "doc": "One or more genomic intervals over which to operate", "id": "#GATK-PrintReads.cwl/intervals" }, { "type": "string", "default": "-Xmx4g", "inputBinding": { "position": 0 }, "id": "#GATK-PrintReads.cwl/java_arg" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--number" }, "doc": "Exclude all reads with this platform from the output", "id": "#GATK-PrintReads.cwl/number" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "-o" }, "doc": "name of the output file from indelRealigner", "id": "#GATK-PrintReads.cwl/outputfile_printReads" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--platform" }, "doc": "Exclude all reads with this platform from the output", "id": "#GATK-PrintReads.cwl/platform" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "--readGroup" }, "doc": "Exclude all reads with this read group from the output", "id": "#GATK-PrintReads.cwl/readGroup" }, { "type": "File", "inputBinding": { "position": 2, "prefix": "-R" }, "secondaryFiles": [ ".amb", ".ann", ".bwt", ".pac", ".sa", ".fai", "^.dict" ], "id": "#GATK-PrintReads.cwl/reference" }, { "type": [ "null", { "type": "array", "items": "File" } ], "inputBinding": { "position": 2 }, "id": "#GATK-PrintReads.cwl/sample_file" }, { "type": [ "null", { "type": "array", "items": "string" } ], "inputBinding": { "position": 2 }, "doc": "Sample name to be included in the analysis. Can be specified multiple times.", "id": "#GATK-PrintReads.cwl/sample_name" }, { "type": [ "null", "boolean" ], "inputBinding": { "position": 2, "prefix": "--simplify" }, "doc": "Erase all extra attributes in the read but keep the read group information", "id": "#GATK-PrintReads.cwl/simplify" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.outputfile_printReads)" }, "secondaryFiles": [ "^.bai" ], "id": "#GATK-PrintReads.cwl/output_printReads" } ], "arguments": [ { "valueFrom": "$(runtime.tmpdir)", "position": 0, "separate": false, "prefix": "-Djava.io.tmpdir=" }, { "valueFrom": "PrintReads", "position": 2, "prefix": "-T" } ], "baseCommand": [ "java" ], "doc": "GATK-RealignTargetCreator.cwl is developed for CWL consortium\nPrints all reads that have a mapping quality above zero\n Usage: java -Xmx4g -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input1.bam -I input2.bam -o output.bam --read_filter MappingQualityZero\n", "id": "#GATK-PrintReads.cwl" }, { "class": "CommandLineTool", "doc": "GATK-VariantsRecalibrator.cwl is developed for CWL consortium\n\nUsage:\n```\njava -Xmx8G \\\n -jar gatk.jar\n -T VariantRecalibrator \\\n -R [reference_fasta] \\\n -recalFile $tmpDir/out.recal \\\n -tranchesFile $tmpDir/out.tranches \\\n -rscriptFile $tmpDir/out.R \\\n -nt 4 \\\n -an MQRankSum -an ReadPosRankSum -an DP -an FS -an QD \\\n -mode SNP \\\n -resource:hapmap,known=false,training=true,truth=true,prior=15.0 [hapmap_vcf] \\\n -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 [dbsnp_vcf] \\\n -resource:omni,known=false,training=true,truth=true,prior=12.0 [1komni_vcf] \\\n -resource:1000G,known=false,training=true,truth=false,prior=10.0 [1ksnp_vcf]\n```\n", "requirements": [ { "$import": "#envvar-global.yml" }, { "class": "DockerRequirement", "dockerPull": "dukegcb/gatk-base:3" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "3.8" ], "package": "gatk", "https://schema.org/citation": "https://dx.doi.org/10.1038/ng.806" } ] } ], "inputs": [ { "type": "File", "inputBinding": { "position": 1, "prefix": "-jar" }, "id": "#GATK-VariantRecalibrator-Indels.cwl/GATKJar" }, { "type": { "type": "array", "items": "string", "inputBinding": { "prefix": "-an" } }, "inputBinding": { "position": 2 }, "doc": "The names of the annotations which should used for calculations", "id": "#GATK-VariantRecalibrator-Indels.cwl/annotations" }, { "type": [ "null", { "type": "array", "items": "File" } ], "inputBinding": { "position": 2, "prefix": "--intervals" }, "doc": "One or more genomic intervals over which to operate", "id": "#GATK-VariantRecalibrator-Indels.cwl/intervals" }, { "type": "string", "default": "-Xmx8g", "inputBinding": { "position": 0 }, "id": "#GATK-VariantRecalibrator-Indels.cwl/java_arg" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--maxGaussians" }, "doc": "Maximum number of different clusters (gaussians) of variants the program is allowed to try to identify.", "id": "#GATK-VariantRecalibrator-Indels.cwl/max_gaussians" }, { "type": "string", "inputBinding": { "position": 2, "prefix": "-recalFile" }, "id": "#GATK-VariantRecalibrator-Indels.cwl/outputfile_recal" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "-rscriptFile" }, "id": "#GATK-VariantRecalibrator-Indels.cwl/outputfile_rscript" }, { "type": "string", "inputBinding": { "position": 2, "prefix": "-tranchesFile" }, "id": "#GATK-VariantRecalibrator-Indels.cwl/outputfile_tranches" }, { "type": "File", "secondaryFiles": [ ".fai", "^.dict" ], "inputBinding": { "position": 2, "prefix": "-R" }, "doc": "reference genome", "id": "#GATK-VariantRecalibrator-Indels.cwl/reference" }, { "type": "File", "secondaryFiles": [ ".idx" ], "inputBinding": { "position": 2, "prefix": "-resource:dbsnp,known=true,training=false,truth=false,prior=2.0" }, "doc": "dbSNP reference data", "id": "#GATK-VariantRecalibrator-Indels.cwl/resource_dbsnp" }, { "type": "File", "secondaryFiles": [ ".idx" ], "inputBinding": { "position": 2, "prefix": "-resource:mills,known=false,training=true,truth=true,prior=12.0" }, "doc": "hapmap reference data", "id": "#GATK-VariantRecalibrator-Indels.cwl/resource_mills" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "-nt" }, "doc": "Number of data threads to allocate to this analysis", "id": "#GATK-VariantRecalibrator-Indels.cwl/threads" }, { "type": "File", "secondaryFiles": [ ".idx" ], "inputBinding": { "position": 2, "prefix": "-input" }, "doc": "input vcf File raw variant calls from haplotype caller", "id": "#GATK-VariantRecalibrator-Indels.cwl/variants" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.outputfile_recal)" }, "secondaryFiles": [ ".pdf" ], "doc": "the recal File", "id": "#GATK-VariantRecalibrator-Indels.cwl/recal_File" }, { "type": "File", "outputBinding": { "glob": "$(inputs.outputfile_tranches)" }, "secondaryFiles": [ ".pdf" ], "doc": "the tranches File", "id": "#GATK-VariantRecalibrator-Indels.cwl/tranches_File" }, { "type": [ "null", "File" ], "outputBinding": { "glob": "$(inputs.outputfile_rscript)" }, "secondaryFiles": [ ".pdf" ], "doc": "The output recalibration R script for the plots", "id": "#GATK-VariantRecalibrator-Indels.cwl/vqsr_rscript" } ], "arguments": [ { "valueFrom": "$(runtime.tmpdir)", "position": 0, "separate": false, "prefix": "-Djava.io.tmpdir=" }, { "valueFrom": "VariantRecalibrator", "position": 2, "prefix": "-T" }, { "valueFrom": "INDEL", "position": 2, "prefix": "-mode" } ], "baseCommand": [ "java" ], "id": "#GATK-VariantRecalibrator-Indels.cwl" }, { "class": "CommandLineTool", "doc": "GATK-VariantsRecalibrator.cwl is developed for CWL consortium\n\nUsage:\n```\njava -Xmx8G \\\n -jar gatk.jar\n -T VariantRecalibrator \\\n -R [reference_fasta] \\\n -recalFile $tmpDir/out.recal \\\n -tranchesFile $tmpDir/out.tranches \\\n -rscriptFile $tmpDir/out.R \\\n -nt 4 \\\n -an MQRankSum -an ReadPosRankSum -an DP -an FS -an QD \\\n -mode SNP \\\n -resource:hapmap,known=false,training=true,truth=true,prior=15.0 [hapmap_vcf] \\\n -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 [dbsnp_vcf] \\\n -resource:omni,known=false,training=true,truth=true,prior=12.0 [1komni_vcf] \\\n -resource:1000G,known=false,training=true,truth=false,prior=10.0 [1ksnp_vcf]\n```\n", "requirements": [ { "$import": "#envvar-global.yml" }, { "class": "DockerRequirement", "dockerPull": "dukegcb/gatk-base:3" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "3.8" ], "package": "gatk", "https://schema.org/citation": "https://dx.doi.org/10.1038/ng.806" } ] } ], "inputs": [ { "type": "File", "inputBinding": { "position": 1, "prefix": "-jar" }, "id": "#GATK-VariantRecalibrator-SNPs.cwl/GATKJar" }, { "type": { "type": "array", "items": "string", "inputBinding": { "prefix": "-an" } }, "inputBinding": { "position": 2 }, "doc": "The names of the annotations which should used for calculations", "id": "#GATK-VariantRecalibrator-SNPs.cwl/annotations" }, { "type": [ "null", { "type": "array", "items": "File" } ], "inputBinding": { "position": 2, "prefix": "--intervals" }, "doc": "One or more genomic intervals over which to operate", "id": "#GATK-VariantRecalibrator-SNPs.cwl/intervals" }, { "type": "string", "default": "-Xmx8g", "inputBinding": { "position": 0 }, "id": "#GATK-VariantRecalibrator-SNPs.cwl/java_arg" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "--maxGaussians" }, "doc": "Maximum number of different clusters (gaussians) of variants the program is allowed to try to identify.", "id": "#GATK-VariantRecalibrator-SNPs.cwl/max_gaussians" }, { "type": "string", "inputBinding": { "position": 2, "prefix": "-recalFile" }, "id": "#GATK-VariantRecalibrator-SNPs.cwl/outputfile_recal" }, { "type": [ "null", "string" ], "inputBinding": { "position": 2, "prefix": "-rscriptFile" }, "id": "#GATK-VariantRecalibrator-SNPs.cwl/outputfile_rscript" }, { "type": "string", "inputBinding": { "position": 2, "prefix": "-tranchesFile" }, "id": "#GATK-VariantRecalibrator-SNPs.cwl/outputfile_tranches" }, { "type": "File", "secondaryFiles": [ ".fai", "^.dict" ], "inputBinding": { "position": 2, "prefix": "-R" }, "doc": "reference genome", "id": "#GATK-VariantRecalibrator-SNPs.cwl/reference" }, { "type": "File", "secondaryFiles": [ ".idx" ], "inputBinding": { "position": 2, "prefix": "-resource:1000G,known=false,training=true,truth=false,prior=10.0" }, "doc": "1000 genome reference data", "id": "#GATK-VariantRecalibrator-SNPs.cwl/resource_1kg" }, { "type": "File", "secondaryFiles": [ ".idx" ], "inputBinding": { "position": 2, "prefix": "-resource:dbsnp,known=true,training=false,truth=false,prior=2.0" }, "doc": "dbSNP reference data", "id": "#GATK-VariantRecalibrator-SNPs.cwl/resource_dbsnp" }, { "type": "File", "secondaryFiles": [ ".idx" ], "inputBinding": { "position": 2, "prefix": "-resource:hapmap,known=false,training=true,truth=true,prior=15.0" }, "doc": "hapmap reference data", "id": "#GATK-VariantRecalibrator-SNPs.cwl/resource_hapmap" }, { "type": "File", "secondaryFiles": [ ".idx" ], "inputBinding": { "position": 2, "prefix": "-resource:omni,known=false,training=true,truth=false,prior=12.0" }, "doc": "omni reference data", "id": "#GATK-VariantRecalibrator-SNPs.cwl/resource_omni" }, { "type": [ "null", "int" ], "inputBinding": { "position": 2, "prefix": "-nt" }, "doc": "Number of data threads to allocate to this analysis", "id": "#GATK-VariantRecalibrator-SNPs.cwl/threads" }, { "type": "File", "secondaryFiles": [ ".idx" ], "inputBinding": { "position": 2, "prefix": "-input" }, "doc": "input vcf File raw variant calls from haplotype caller", "id": "#GATK-VariantRecalibrator-SNPs.cwl/variants" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.outputfile_recal)" }, "secondaryFiles": [ ".pdf" ], "doc": "the recal File", "id": "#GATK-VariantRecalibrator-SNPs.cwl/recal_File" }, { "type": "File", "outputBinding": { "glob": "$(inputs.outputfile_tranches)" }, "secondaryFiles": [ ".pdf" ], "doc": "the tranches File", "id": "#GATK-VariantRecalibrator-SNPs.cwl/tranches_File" }, { "type": [ "null", "File" ], "outputBinding": { "glob": "$(inputs.outputfile_rscript)" }, "secondaryFiles": [ ".pdf" ], "doc": "The output recalibration R script for the plots", "id": "#GATK-VariantRecalibrator-SNPs.cwl/vqsr_rscript" } ], "arguments": [ { "valueFrom": "$(runtime.tmpdir)", "position": 0, "separate": false, "prefix": "-Djava.io.tmpdir=" }, { "valueFrom": "VariantRecalibrator", "position": 2, "prefix": "-T" }, { "valueFrom": "SNP", "position": 2, "prefix": "-mode" } ], "baseCommand": [ "java" ], "id": "#GATK-VariantRecalibrator-SNPs.cwl" }, { "class": "CommandLineTool", "requirements": [ { "$import": "#envvar-global.yml" }, { "class": "DockerRequirement", "dockerPull": "dukegcb/bwa-samtools:0.7.12_1.2.1-254-6462e34" }, { "class": "InlineJavascriptRequirement" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "0.7.12" ], "package": "bwa", "https://schema.org/citation": "https://dx.doi.org/10.1093/bioinformatics/btp324" }, { "version": [ "1.2-242-g4d56437" ], "package": "samtools", "https://schema.org/citation": "https://doi.org/10.1093/bioinformatics/btp352" } ] } ], "inputs": [ { "type": [ "null", { "type": "array", "items": "int" } ], "inputBinding": { "position": 1, "prefix": "-I", "itemSeparator": "," }, "id": "#bwa-mem-samtools.cwl/min_std_max_min" }, { "type": [ "null", "int" ], "inputBinding": { "position": 1, "prefix": "-k" }, "doc": "-k INT minimum seed length [19]", "id": "#bwa-mem-samtools.cwl/minimum_seed_length" }, { "type": "string", "id": "#bwa-mem-samtools.cwl/output_filename" }, { "type": [ "null", "string" ], "inputBinding": { "position": 1, "prefix": "-R" }, "doc": "-R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]", "id": "#bwa-mem-samtools.cwl/read_group_header" }, { "type": { "type": "array", "items": "File" }, "inputBinding": { "position": 3 }, "id": "#bwa-mem-samtools.cwl/reads" }, { "type": "File", "inputBinding": { "position": 2 }, "secondaryFiles": [ ".amb", ".ann", ".bwt", ".pac", ".sa" ], "id": "#bwa-mem-samtools.cwl/reference" }, { "type": [ "null", "int" ], "inputBinding": { "position": 1, "prefix": "-t" }, "doc": "-t INT number of threads [1]", "id": "#bwa-mem-samtools.cwl/threads" } ], "stdout": "$(inputs.output_filename)", "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.output_filename)" }, "id": "#bwa-mem-samtools.cwl/output" } ], "baseCommand": [ "bwamem-to-samtools.sh" ], "doc": "Usage: bwa mem [options] [in2.fq]\n\nAlgorithm options:\n -w INT band width for banded alignment [100]\n -d INT off-diagonal X-dropoff [100]\n -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]\n -y INT seed occurrence for the 3rd round seeding [20]\n -c INT skip seeds with more than INT occurrences [500]\n -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]\n -W INT discard a chain if seeded bases shorter than INT [0]\n -m INT perform at most INT rounds of mate rescues for each read [50]\n -S skip mate rescue\n -P skip pairing; mate rescue performed unless -S also in use\n -e discard full-length exact matches\n\nScoring options:\n\n -A INT score for a sequence match, which scales options -TdBOELU unless overridden [1]\n -B INT penalty for a mismatch [4]\n -O INT[,INT] gap open penalties for deletions and insertions [6,6]\n -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1]\n -L INT[,INT] penalty for 5'- and 3'-end clipping [5,5]\n -U INT penalty for an unpaired read pair [17]\n\n -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 (PacBio reads to ref)\n ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 (Oxford Nanopore 2D-reads to ref)\n intractg: -B9 -O16 -L5 (intra-species contigs to ref)\n\nInput/output options:\n\n -p smart pairing (ignoring in2.fq)\n -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n -H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null]\n -j treat ALT contigs as part of the primary assembly (i.e. ignore .alt file)\n\n -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]\n -T INT minimum score to output [30]\n -h INT[,INT] if there are 80% of the max score, output all in XA [5,200]\n -a output all alignments for SE or unpaired PE\n -C append FASTA/FASTQ comment to SAM output\n -V output the reference FASTA header in the XR tag\n -Y use soft clipping for supplementary alignments\n -M mark shorter split hits as secondary\n\n -I FLOAT[,FLOAT[,INT[,INT]]]\n specify the mean, standard deviation (10% of the mean if absent), max\n (4 sigma from the mean if absent) and min of the insert size distribution.\n FR orientation only. [inferred]\n\nNote: Please read the man page for detailed description of the command line and options.\n", "id": "#bwa-mem-samtools.cwl" }, { "class": "ExpressionTool", "label": "Given a NamedFASTQFilePairType returns an array of the files contained within", "requirements": [ { "class": "InlineJavascriptRequirement" }, { "$import": "#bespin-types.yml" } ], "inputs": [ { "type": "string", "id": "#extract-named-file-pair-details.cwl/library" }, { "type": "string", "id": "#extract-named-file-pair-details.cwl/platform" }, { "type": "#bespin-types.yml/NamedFASTQFilePairType", "id": "#extract-named-file-pair-details.cwl/read_pair" } ], "outputs": [ { "type": "string", "id": "#extract-named-file-pair-details.cwl/read_group_header" }, { "type": "string", "id": "#extract-named-file-pair-details.cwl/read_pair_name" }, { "type": { "type": "array", "items": "File" }, "id": "#extract-named-file-pair-details.cwl/reads" } ], "expression": "${\n var readPairName = inputs.read_pair.name;\n var readGroupHeader = \"@RG\" +\n \"\\\\tID:\" + readPairName +\n \"\\\\tLB:\" + inputs.library +\n \"\\\\tPL:\" + inputs.platform +\n \"\\\\tPU:\" + readPairName +\n \"\\\\tSM:\" + readPairName;\n return {\n reads: [\n inputs.read_pair.file1,\n inputs.read_pair.file2,\n ],\n read_pair_name: readPairName,\n read_group_header: readGroupHeader\n };\n\n}\n", "id": "#extract-named-file-pair-details.cwl" }, { "class": "CommandLineTool", "hints": [ { "class": "DockerRequirement", "dockerPull": "dukegcb/fastqc:0.11.4" }, { "class": "SoftwareRequirement", "packages": [ { "version": [ "0.11.4" ], "package": "fastqc", "https://schema.org/citation": "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" } ] } ], "requirements": [ { "class": "InlineJavascriptRequirement" } ], "inputs": [ { "type": "string", "default": "fastq", "inputBinding": { "position": 3, "prefix": "--format" }, "id": "#fastqc.cwl/format" }, { "type": "File", "inputBinding": { "position": 4 }, "id": "#fastqc.cwl/input_fastq_file" }, { "type": "boolean", "default": true, "inputBinding": { "prefix": "--noextract", "position": 2 }, "id": "#fastqc.cwl/noextract" }, { "type": "int", "default": 1, "inputBinding": { "position": 5, "prefix": "--threads" }, "id": "#fastqc.cwl/threads" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "*_fastqc.zip" }, "id": "#fastqc.cwl/output_qc_report" } ], "baseCommand": "fastqc", "arguments": [ { "valueFrom": "$('/tmp')", "prefix": "--dir", "position": 5 }, { "valueFrom": "$(runtime.outdir)", "prefix": "-o", "position": 5 } ], "id": "#fastqc.cwl" }, { "class": "ExpressionTool", "label": "Moves an array of File pairs into a named directory", "requirements": [ { "class": "InlineJavascriptRequirement" } ], "inputs": [ { "type": { "type": "array", "items": { "type": "array", "items": "File" } }, "id": "#file-pairs-to-directory.cwl/file_pairs" }, { "type": "string", "id": "#file-pairs-to-directory.cwl/name" } ], "outputs": [ { "type": "Directory", "id": "#file-pairs-to-directory.cwl/outdir" } ], "expression": "${\n var files = inputs.file_pairs.reduce(function(a,b) {\n return a.concat(b);\n }, []);\n\n var result = {\n outdir: {\n class: 'Directory',\n basename: inputs.name,\n listing: files\n }\n };\n\n return result;\n}\n", "id": "#file-pairs-to-directory.cwl" }, { "class": "ExpressionTool", "label": "Moves an array of Files into a named directory", "requirements": [ { "class": "InlineJavascriptRequirement" } ], "inputs": [ { "type": { "type": "array", "items": "File" }, "id": "#files-to-directory.cwl/files" }, { "type": "string", "id": "#files-to-directory.cwl/name" } ], "outputs": [ { "type": "Directory", "id": "#files-to-directory.cwl/outdir" } ], "expression": "${\n var result = {\n outdir: {\n class: 'Directory',\n basename: inputs.name,\n listing: inputs.files\n }\n };\n\n return result;\n}\n", "id": "#files-to-directory.cwl" }, { "class": "ExpressionTool", "label": "Generates a set of file names for joint steps based on an input name", "requirements": [ { "class": "InlineJavascriptRequirement" } ], "inputs": [ { "type": "string", "id": "#generate-joint-filenames.cwl/name" } ], "outputs": [ { "type": "string", "id": "#generate-joint-filenames.cwl/joint_genotype_raw_variants_output_filename" }, { "type": "string", "id": "#generate-joint-filenames.cwl/snps_indels_recalibrated_output_filename" }, { "type": "string", "id": "#generate-joint-filenames.cwl/snps_indels_vqsr_recal_output_filename" }, { "type": "string", "id": "#generate-joint-filenames.cwl/snps_indels_vqsr_rscript_output_filename" }, { "type": "string", "id": "#generate-joint-filenames.cwl/snps_indels_vqsr_tranches_output_filename" }, { "type": "string", "id": "#generate-joint-filenames.cwl/snps_recalibrated_output_filename" }, { "type": "string", "id": "#generate-joint-filenames.cwl/snps_vqsr_recal_output_filename" }, { "type": "string", "id": "#generate-joint-filenames.cwl/snps_vqsr_rscript_output_filename" }, { "type": "string", "id": "#generate-joint-filenames.cwl/snps_vqsr_tranches_output_filename" } ], "expression": "${\n function makeFilename(base, suffix, extension) {\n return base + '-' + suffix + '.' + extension;\n }\n var base = inputs.name\n\n return {\n joint_genotype_raw_variants_output_filename: makeFilename(base, 'raw_variants', 'g.vcf'),\n snps_vqsr_recal_output_filename: makeFilename(base, 'snps_vqsr_recal', 'out'),\n snps_vqsr_tranches_output_filename: makeFilename(base, 'snps_vqsr_tranches', 'out'),\n snps_vqsr_rscript_output_filename: makeFilename(base, 'snps_vqsr', 'R'),\n snps_recalibrated_output_filename: makeFilename(base, 'snps_recalibrated', 'vcf'),\n snps_indels_vqsr_recal_output_filename: makeFilename(base, 'snps_indels_vqsr_recal', 'out'),\n snps_indels_vqsr_tranches_output_filename: makeFilename(base, 'snps_indels_vqsr_tranches', 'out'),\n snps_indels_vqsr_rscript_output_filename: makeFilename(base, 'snps_indels_vqsr', 'R'),\n snps_indels_recalibrated_output_filename: makeFilename(base, 'snps_indels_recalibrated', 'vcf')\n };\n}\n", "id": "#generate-joint-filenames.cwl" }, { "class": "ExpressionTool", "label": "Generates a set of file names for preprocessing steps based on an input sample name", "requirements": [ { "class": "InlineJavascriptRequirement" } ], "inputs": [ { "type": "string", "id": "#generate-sample-filenames.cwl/sample_name" } ], "outputs": [ { "type": "string", "id": "#generate-sample-filenames.cwl/dedup_metrics_output_filename" }, { "type": "string", "id": "#generate-sample-filenames.cwl/dedup_reads_output_filename" }, { "type": "string", "id": "#generate-sample-filenames.cwl/haplotypes_bam_output_filename" }, { "type": "string", "id": "#generate-sample-filenames.cwl/hs_metrics_output_filename" }, { "type": "string", "id": "#generate-sample-filenames.cwl/mapped_reads_output_filename" }, { "type": "string", "id": "#generate-sample-filenames.cwl/raw_variants_output_filename" }, { "type": "string", "id": "#generate-sample-filenames.cwl/recal_reads_output_filename" }, { "type": "string", "id": "#generate-sample-filenames.cwl/recal_table_output_filename" }, { "type": "string", "id": "#generate-sample-filenames.cwl/sorted_reads_output_filename" } ], "expression": "${\n function makeFilename(base, suffix, extension) {\n return base + '-' + suffix + '.' + extension;\n }\n var base = inputs.sample_name\n\n return {\n mapped_reads_output_filename: makeFilename(base, 'mapped', 'bam'),\n sorted_reads_output_filename: makeFilename(base, 'sorted', 'bam'),\n dedup_reads_output_filename: makeFilename(base, 'dedup', 'bam'),\n dedup_metrics_output_filename: makeFilename(base, 'dedup-metrics', 'out'),\n recal_reads_output_filename: makeFilename(base, 'recal', 'bam'),\n recal_table_output_filename: makeFilename(base, 'recal', 'table'),\n raw_variants_output_filename: makeFilename(base, 'raw_variants', 'g.vcf'),\n haplotypes_bam_output_filename: makeFilename(base, 'haplotypes', 'bam'),\n hs_metrics_output_filename: makeFilename(base, 'hs', 'txt')\n };\n}\n", "id": "#generate-sample-filenames.cwl" }, { "class": "ExpressionTool", "label": "Given an ExomeseqStudyType returns an array of the annotations to use.", "doc": "The InbreedingCoeff is a population level statistic that requires at least 10 samples in order to be computed. For projects with fewer samples, or that includes many closely related samples (such as a family) please omit this annotation from the command line. From https://software.broadinstitute.org/gatk/documentation/article?id=1259\n", "requirements": [ { "class": "InlineJavascriptRequirement" }, { "$import": "#bespin-types.yml" } ], "inputs": [ { "type": { "type": "array", "items": "string" }, "id": "#generate-variant-recalibration-annotation-set.cwl/base_annotations" }, { "type": "#bespin-types.yml/ExomeseqStudyType", "id": "#generate-variant-recalibration-annotation-set.cwl/study_type" } ], "outputs": [ { "type": { "type": "array", "items": "string" }, "id": "#generate-variant-recalibration-annotation-set.cwl/annotations" } ], "expression": "${\n var annotations = inputs.base_annotations;\n var inputStudyType = inputs.study_type;\n if(inputStudyType === \"Large Population\") {\n annotations.push(\"InbreedingCoeff\");\n }\n return {\"annotations\": annotations };\n}\n", "id": "#generate-variant-recalibration-annotation-set.cwl" }, { "class": "CommandLineTool", "requirements": [ { "class": "DockerRequirement", "dockerPull": "dukegcb/picard:2.10.7" }, { "class": "InlineJavascriptRequirement" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "2.10.7" ], "package": "picard", "https://schema.org/citation": "http://broadinstitute.github.io/picard" } ] } ], "inputs": [ { "type": [ "null", { "type": "array", "items": "File" } ], "doc": "The bed file to be converted to interval_list format. Required.", "inputBinding": { "prefix": "I=", "shellQuote": false }, "id": "#picard-BedToIntervalList.cwl/input_file" }, { "type": [ "null", "string" ], "doc": "Interval list output filename.", "default": "list.interval_list", "inputBinding": { "prefix": "O=", "shellQuote": false }, "id": "#picard-BedToIntervalList.cwl/output_filename" }, { "type": "File", "doc": "The reference sequences in fasta format.", "inputBinding": { "prefix": "SD=", "shellQuote": false }, "id": "#picard-BedToIntervalList.cwl/reference_sequence" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.output_filename)" }, "id": "#picard-BedToIntervalList.cwl/output_interval_list_file" } ], "baseCommand": [ "java", "-Xmx4g" ], "arguments": [ { "valueFrom": "/opt/picard/picard.jar", "position": -1, "prefix": "-jar" }, { "valueFrom": "BedToIntervalList", "position": 0 } ], "id": "#picard-BedToIntervalList.cwl" }, { "class": "CommandLineTool", "requirements": [ { "class": "DockerRequirement", "dockerPull": "dukegcb/picard:2.10.7" }, { "class": "InlineJavascriptRequirement" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "2.10.7" ], "package": "picard", "https://schema.org/citation": "http://broadinstitute.github.io/picard" } ] } ], "inputs": [ { "type": "File", "doc": "The bait interval file in picard interval_list format (from capture kit).", "inputBinding": { "prefix": "BAIT_INTERVALS=", "shellQuote": false }, "id": "#picard-CollectHsMetrics.cwl/bait_intervals" }, { "type": "File", "doc": "The BAM or SAM file to collect metrics from. Required.", "inputBinding": { "prefix": "I=", "shellQuote": false }, "id": "#picard-CollectHsMetrics.cwl/input_file" }, { "type": [ "null", "string" ], "doc": "The metrics output filename.", "default": "hs_metrics.txt", "inputBinding": { "prefix": "O=", "shellQuote": false }, "id": "#picard-CollectHsMetrics.cwl/output_filename" }, { "type": "File", "doc": "The reference sequences in fasta format.", "inputBinding": { "prefix": "R=", "shellQuote": false }, "id": "#picard-CollectHsMetrics.cwl/reference_sequence" }, { "type": "File", "doc": "The target interval file in picard interval_list format (from capture kit).", "inputBinding": { "prefix": "TARGET_INTERVALS=", "shellQuote": false }, "id": "#picard-CollectHsMetrics.cwl/target_intervals" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.output_filename)" }, "id": "#picard-CollectHsMetrics.cwl/output_hs_metrics_file" } ], "baseCommand": [ "java", "-Xmx4g" ], "arguments": [ { "valueFrom": "/opt/picard/picard.jar", "position": -1, "prefix": "-jar" }, { "valueFrom": "CollectHsMetrics", "position": 0 } ], "id": "#picard-CollectHsMetrics.cwl" }, { "class": "CommandLineTool", "requirements": [ { "class": "DockerRequirement", "dockerPull": "dukegcb/picard:2.10.7" }, { "class": "InlineJavascriptRequirement" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "2.10.7" ], "package": "picard", "https://schema.org/citation": "http://broadinstitute.github.io/picard" } ] } ], "inputs": [ { "type": "File", "doc": "One or more input SAM or BAM files to analyze. Must be coordinate sorted.", "inputBinding": { "prefix": "INPUT=", "shellQuote": false }, "id": "#picard-MarkDuplicates.cwl/input_file" }, { "type": [ "null", "string" ], "doc": "Output metrics filename", "default": "marked_dup_metrics.txt", "inputBinding": { "prefix": "METRICS_FILE=", "shellQuote": false }, "id": "#picard-MarkDuplicates.cwl/metrics_filename" }, { "type": [ "null", "string" ], "doc": "Output filename", "default": "marked_duplicates.bam", "inputBinding": { "prefix": "OUTPUT=", "shellQuote": false }, "id": "#picard-MarkDuplicates.cwl/output_filename" }, { "type": "boolean", "doc": "If true do not write duplicates to the output file instead of writing them with appropriate flags set. (Default true).", "default": true, "inputBinding": { "prefix": "REMOVE_DUPLICATES=", "shellQuote": false }, "id": "#picard-MarkDuplicates.cwl/remove_duplicates" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.output_filename)" }, "secondaryFiles": [ "^.bai" ], "id": "#picard-MarkDuplicates.cwl/output_dedup_bam_file" }, { "type": "File", "outputBinding": { "glob": "$(inputs.metrics_filename)" }, "id": "#picard-MarkDuplicates.cwl/output_metrics_file" } ], "baseCommand": [ "java" ], "arguments": [ { "valueFrom": "-Xmx4g", "position": -2 }, { "valueFrom": "/opt/picard/picard.jar", "position": -1, "prefix": "-jar" }, { "valueFrom": "MarkDuplicates", "position": 0 }, { "valueFrom": "CREATE_INDEX=True", "position": 0 } ], "id": "#picard-MarkDuplicates.cwl" }, { "class": "CommandLineTool", "requirements": [ { "class": "DockerRequirement", "dockerPull": "dukegcb/picard:2.10.7" }, { "class": "InlineJavascriptRequirement" } ], "hints": [ { "class": "SoftwareRequirement", "packages": [ { "version": [ "2.10.7" ], "package": "picard", "https://schema.org/citation": "http://broadinstitute.github.io/picard" } ] } ], "inputs": [ { "type": "File", "doc": "The BAM or SAM file to sort. Required.", "inputBinding": { "prefix": "INPUT=", "shellQuote": false }, "id": "#picard-SortSam.cwl/input_file" }, { "type": [ "null", "string" ], "doc": "The sorted BAM or SAM output file.", "default": "sorted.bam", "inputBinding": { "prefix": "OUTPUT=", "shellQuote": false }, "id": "#picard-SortSam.cwl/output_filename" }, { "type": "string", "doc": "Sort order of output file Required. Possible values: {unsorted, queryname, coordinate, duplicate}", "default": "coordinate", "inputBinding": { "prefix": "SORT_ORDER=", "shellQuote": false }, "id": "#picard-SortSam.cwl/sort_order" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "$(inputs.output_filename)" }, "secondaryFiles": [ "^.bai" ], "id": "#picard-SortSam.cwl/sorted" } ], "baseCommand": [ "java", "-Xmx4g" ], "arguments": [ { "valueFrom": "/opt/picard/picard.jar", "position": -1, "prefix": "-jar" }, { "valueFrom": "SortSam", "position": 0 } ], "id": "#picard-SortSam.cwl" }, { "class": "CommandLineTool", "hints": [ { "class": "DockerRequirement", "dockerPull": "dukegcb/trim-galore:0.4.4" }, { "class": "SoftwareRequirement", "packages": [ { "version": [ "1.14" ], "package": "cutadapt", "https://schema.org/citation": "https://dx.doi.org/10.14806/ej.17.1.200" }, { "version": [ "0.4.4" ], "package": "trimgalore", "https://schema.org/citation": "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/" } ] } ], "inputs": [ { "type": "boolean", "inputBinding": { "position": 1, "prefix": "--paired" }, "id": "#trim_galore.cwl/paired" }, { "type": { "type": "array", "items": "File" }, "inputBinding": { "position": 3 }, "id": "#trim_galore.cwl/reads" } ], "outputs": [ { "type": { "type": "array", "items": "File" }, "outputBinding": { "glob": "*_trimming_report.txt" }, "id": "#trim_galore.cwl/trim_reports" }, { "type": { "type": "array", "items": "File" }, "outputBinding": { "glob": "*_val_*.fq*" }, "id": "#trim_galore.cwl/trimmed_reads" } ], "baseCommand": "trim_galore", "arguments": [ { "valueFrom": "$(runtime.outdir)", "prefix": "-o", "position": 2 } ], "id": "#trim_galore.cwl" }, { "class": "Workflow", "label": "Whole Exome Sequencing", "doc": "Whole Exome Sequence analysis using GATK best practices - Germline SNP & Indel Discovery\n", "requirements": [ { "class": "ScatterFeatureRequirement" }, { "class": "SubworkflowFeatureRequirement" }, { "$import": "#bespin-types.yml" } ], "inputs": [ { "type": "File", "id": "#main/GATKJar" }, { "type": "File", "secondaryFiles": [ ".idx" ], "id": "#main/indel_resource_mills" }, { "type": [ "null", "int" ], "id": "#main/interval_padding" }, { "type": [ "null", { "type": "array", "items": "File" } ], "id": "#main/intervals" }, { "type": { "type": "array", "items": "File" }, "secondaryFiles": [ ".idx" ], "id": "#main/knownSites" }, { "type": "string", "id": "#main/library" }, { "type": "string", "id": "#main/platform" }, { "type": [ "null", { "type": "array", "items": "File" } ], "id": "#main/primary_intervals" }, { "type": { "type": "array", "items": "#bespin-types.yml/NamedFASTQFilePairType" }, "id": "#main/read_pairs" }, { "type": "File", "secondaryFiles": [ ".amb", ".ann", ".bwt", ".pac", ".sa", ".fai", "^.dict" ], "id": "#main/reference_genome" }, { "type": "File", "secondaryFiles": [ ".idx" ], "id": "#main/resource_dbsnp" }, { "type": "File", "secondaryFiles": [ ".idx" ], "id": "#main/snp_resource_1kg" }, { "type": "File", "secondaryFiles": [ ".idx" ], "id": "#main/snp_resource_hapmap" }, { "type": "File", "secondaryFiles": [ ".idx" ], "id": "#main/snp_resource_omni" }, { "type": "#bespin-types.yml/ExomeseqStudyType", "id": "#main/study_type" }, { "type": [ "null", "int" ], "id": "#main/threads" } ], "outputs": [ { "type": "Directory", "outputSource": "#main/organize_directories/bams_final_dir", "doc": "BAM files containing assembled haplotypes and locally realigned reads", "id": "#main/bams_final_dir" }, { "type": "Directory", "outputSource": "#main/organize_directories/bams_markduplicates_dir", "doc": "BAM and bai files from markduplicates", "id": "#main/bams_markduplicates_dir" }, { "type": "Directory", "outputSource": "#main/organize_directories/fastqc_reports_dir", "id": "#main/fastqc_reports_dir" }, { "type": "File", "outputSource": "#main/variant_discovery/variant_recalibration_snps_indels_vcf", "doc": "The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value", "id": "#main/filtered_recalibrated_variants" }, { "type": "Directory", "outputSource": "#main/organize_directories/hs_metrics_dir", "id": "#main/hs_metrics_dir" }, { "type": "File", "outputSource": "#main/variant_discovery/joint_raw_variants", "doc": "GVCF file from joint genotyping calling", "id": "#main/joint_raw_variants" }, { "type": "Directory", "outputSource": "#main/organize_directories/raw_variants_dir", "id": "#main/raw_variants_dir" }, { "type": "Directory", "outputSource": "#main/organize_directories/trim_reports_dir", "id": "#main/trim_reports_dir" } ], "steps": [ { "run": "#exomeseq-03-organizedirectories.cwl", "in": [ { "source": "#main/preprocessing/haplotypes_bam", "id": "#main/organize_directories/bams_final" }, { "source": "#main/preprocessing/markduplicates_bam", "id": "#main/organize_directories/bams_markduplicates" }, { "source": "#main/preprocessing/fastqc_reports", "id": 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