Commit d90ba499 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added biopet config values to general gatk trait

parent a148d687
......@@ -24,59 +24,59 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
/** Emit a log entry (level INFO) containing the full list of sequence data files to be included in the analysis (including files inside .bam.list or .cram.list files). */
@Argument(fullName = "showFullBamList", shortName = "", doc = "Emit a log entry (level INFO) containing the full list of sequence data files to be included in the analysis (including files inside .bam.list or .cram.list files).", required = false, exclusiveOf = "", validation = "")
var showFullBamList: Boolean = _
var showFullBamList: Boolean = config("showFullBamList", default = false)
/** Number of reads per SAM file to buffer in memory */
@Argument(fullName = "read_buffer_size", shortName = "rbs", doc = "Number of reads per SAM file to buffer in memory", required = false, exclusiveOf = "", validation = "")
var read_buffer_size: Option[Int] = None
var read_buffer_size: Option[Int] = config("read_buffer_size")
/** Run reporting mode */
@Argument(fullName = "phone_home", shortName = "et", doc = "Run reporting mode", required = false, exclusiveOf = "", validation = "")
var phone_home: org.broadinstitute.gatk.engine.phonehome.GATKRunReport.PhoneHomeOption = _
var phone_home: Option[String] = config("phone_home")
/** GATK key file required to run with -et NO_ET */
@Argument(fullName = "gatk_key", shortName = "K", doc = "GATK key file required to run with -et NO_ET", required = false, exclusiveOf = "", validation = "")
var gatk_key: File = _
@Input(fullName = "gatk_key", shortName = "K", doc = "GATK key file required to run with -et NO_ET", required = false, exclusiveOf = "", validation = "")
var gatk_key: Option[File] = config("gatk_key")
/** Tag to identify this GATK run as part of a group of runs */
@Argument(fullName = "tag", shortName = "tag", doc = "Tag to identify this GATK run as part of a group of runs", required = false, exclusiveOf = "", validation = "")
var tag: String = _
var tag: Option[String] = config("tag")
/** Filters to apply to reads before analysis */
@Argument(fullName = "read_filter", shortName = "rf", doc = "Filters to apply to reads before analysis", required = false, exclusiveOf = "", validation = "")
var read_filter: Seq[String] = Nil
var read_filter: List[String] = config("read_filter", default = Nil)
/** Read filters to disable */
@Argument(fullName = "disable_read_filter", shortName = "drf", doc = "Read filters to disable", required = false, exclusiveOf = "", validation = "")
var disable_read_filter: Seq[String] = Nil
var disable_read_filter: List[String] = config("disable_read_filter", default = Nil)
/** One or more genomic intervals over which to operate */
@Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate", required = false, exclusiveOf = "intervalsString", validation = "")
var intervals: Seq[File] = Nil
var intervals: List[File] = config("intervals", default = Nil)
/** One or more genomic intervals over which to operate */
@Argument(fullName = "intervalsString", shortName = "L", doc = "One or more genomic intervals over which to operate", required = false, exclusiveOf = "intervals", validation = "")
var intervalsString: Seq[String] = Nil
var intervalsString: List[String] = config("intervalsString", default = Nil)
/** One or more genomic intervals to exclude from processing */
@Input(fullName = "excludeIntervals", shortName = "XL", doc = "One or more genomic intervals to exclude from processing", required = false, exclusiveOf = "excludeIntervalsString", validation = "")
var excludeIntervals: Seq[File] = Nil
var excludeIntervals: List[File] = config("excludeIntervals", default = Nil)
/** One or more genomic intervals to exclude from processing */
@Argument(fullName = "excludeIntervalsString", shortName = "XL", doc = "One or more genomic intervals to exclude from processing", required = false, exclusiveOf = "excludeIntervals", validation = "")
var excludeIntervalsString: Seq[String] = Nil
var excludeIntervalsString: List[String] = config("excludeIntervalsString", default = Nil)
/** Set merging approach to use for combining interval inputs */
@Argument(fullName = "interval_set_rule", shortName = "isr", doc = "Set merging approach to use for combining interval inputs", required = false, exclusiveOf = "", validation = "")
var interval_set_rule: org.broadinstitute.gatk.utils.interval.IntervalSetRule = _
var interval_set_rule: Option[String] = config("interval_set_rule")
/** Interval merging rule for abutting intervals */
@Argument(fullName = "interval_merging", shortName = "im", doc = "Interval merging rule for abutting intervals", required = false, exclusiveOf = "", validation = "")
var interval_merging: org.broadinstitute.gatk.utils.interval.IntervalMergingRule = _
var interval_merging: Option[String] = config("interval_merging")
/** Amount of padding (in bp) to add to each interval */
@Argument(fullName = "interval_padding", shortName = "ip", doc = "Amount of padding (in bp) to add to each interval", required = false, exclusiveOf = "", validation = "")
var interval_padding: Option[Int] = None
var interval_padding: Option[Int] = config("interval_padding")
/** Reference sequence file */
@Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false, exclusiveOf = "", validation = "")
......@@ -84,27 +84,27 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
/** Use a non-deterministic random seed */
@Argument(fullName = "nonDeterministicRandomSeed", shortName = "ndrs", doc = "Use a non-deterministic random seed", required = false, exclusiveOf = "", validation = "")
var nonDeterministicRandomSeed: Boolean = _
var nonDeterministicRandomSeed: Boolean = config("nonDeterministicRandomSeed", default = false)
/** Completely eliminates randomized dithering from rank sum tests. */
@Argument(fullName = "disableDithering", shortName = "", doc = "Completely eliminates randomized dithering from rank sum tests.", required = false, exclusiveOf = "", validation = "")
var disableDithering: Boolean = _
var disableDithering: Boolean = config("disableDithering", default = false)
/** Stop execution cleanly as soon as maxRuntime has been reached */
@Argument(fullName = "maxRuntime", shortName = "maxRuntime", doc = "Stop execution cleanly as soon as maxRuntime has been reached", required = false, exclusiveOf = "", validation = "")
var maxRuntime: Option[Long] = None
var maxRuntime: Option[Long] = config("maxRuntime")
/** Unit of time used by maxRuntime */
@Argument(fullName = "maxRuntimeUnits", shortName = "maxRuntimeUnits", doc = "Unit of time used by maxRuntime", required = false, exclusiveOf = "", validation = "")
var maxRuntimeUnits: java.util.concurrent.TimeUnit = _
var maxRuntimeUnits: Option[String] = config("maxRuntimeUnits")
/** Type of read downsampling to employ at a given locus */
@Argument(fullName = "downsampling_type", shortName = "dt", doc = "Type of read downsampling to employ at a given locus", required = false, exclusiveOf = "", validation = "")
var downsampling_type: org.broadinstitute.gatk.utils.downsampling.DownsampleType = _
var downsampling_type: Option[String] = config("downsampling_type")
/** Fraction of reads to downsample to */
@Argument(fullName = "downsample_to_fraction", shortName = "dfrac", doc = "Fraction of reads to downsample to", required = false, exclusiveOf = "", validation = "")
var downsample_to_fraction: Option[Double] = None
var downsample_to_fraction: Option[Double] = config("downsample_to_fraction")
/** Format string for downsample_to_fraction */
@Argument(fullName = "downsample_to_fractionFormat", shortName = "", doc = "Format string for downsample_to_fraction", required = false, exclusiveOf = "", validation = "")
......@@ -112,15 +112,15 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
/** Target coverage threshold for downsampling to coverage */
@Argument(fullName = "downsample_to_coverage", shortName = "dcov", doc = "Target coverage threshold for downsampling to coverage", required = false, exclusiveOf = "", validation = "")
var downsample_to_coverage: Option[Int] = None
var downsample_to_coverage: Option[Int] = config("downsample_to_coverage")
/** Type of BAQ calculation to apply in the engine */
@Argument(fullName = "baq", shortName = "baq", doc = "Type of BAQ calculation to apply in the engine", required = false, exclusiveOf = "", validation = "")
var baq: org.broadinstitute.gatk.utils.baq.BAQ.CalculationMode = _
var baq: Option[String] = config("baq")
/** BAQ gap open penalty */
@Argument(fullName = "baqGapOpenPenalty", shortName = "baqGOP", doc = "BAQ gap open penalty", required = false, exclusiveOf = "", validation = "")
var baqGapOpenPenalty: Option[Double] = None
var baqGapOpenPenalty: Option[Double] = config("baqGapOpenPenalty")
/** Format string for baqGapOpenPenalty */
@Argument(fullName = "baqGapOpenPenaltyFormat", shortName = "", doc = "Format string for baqGapOpenPenalty", required = false, exclusiveOf = "", validation = "")
......@@ -128,59 +128,59 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
/** Reduce NDN elements in CIGAR string */
@Argument(fullName = "refactor_NDN_cigar_string", shortName = "fixNDN", doc = "Reduce NDN elements in CIGAR string", required = false, exclusiveOf = "", validation = "")
var refactor_NDN_cigar_string: Boolean = _
var refactor_NDN_cigar_string: Boolean = config("refactor_NDN_cigar_string", default = false)
/** Fix mis-encoded base quality scores */
@Argument(fullName = "fix_misencoded_quality_scores", shortName = "fixMisencodedQuals", doc = "Fix mis-encoded base quality scores", required = false, exclusiveOf = "", validation = "")
var fix_misencoded_quality_scores: Boolean = _
var fix_misencoded_quality_scores: Boolean = config("fix_misencoded_quality_scores", default = false)
/** Ignore warnings about base quality score encoding */
@Argument(fullName = "allow_potentially_misencoded_quality_scores", shortName = "allowPotentiallyMisencodedQuals", doc = "Ignore warnings about base quality score encoding", required = false, exclusiveOf = "", validation = "")
var allow_potentially_misencoded_quality_scores: Boolean = _
var allow_potentially_misencoded_quality_scores: Boolean = config("allow_potentially_misencoded_quality_scores", default = false)
/** Use the base quality scores from the OQ tag */
@Argument(fullName = "useOriginalQualities", shortName = "OQ", doc = "Use the base quality scores from the OQ tag", required = false, exclusiveOf = "", validation = "")
var useOriginalQualities: Boolean = _
var useOriginalQualities: Boolean = config("useOriginalQualities", default = false)
/** Assign a default base quality */
@Argument(fullName = "defaultBaseQualities", shortName = "DBQ", doc = "Assign a default base quality", required = false, exclusiveOf = "", validation = "")
var defaultBaseQualities: Option[Byte] = None
var defaultBaseQualities: Option[Int] = config("defaultBaseQualities")
/** Write GATK runtime performance log to this file */
@Argument(fullName = "performanceLog", shortName = "PF", doc = "Write GATK runtime performance log to this file", required = false, exclusiveOf = "", validation = "")
var performanceLog: File = _
@Output(fullName = "performanceLog", shortName = "PF", doc = "Write GATK runtime performance log to this file", required = false, exclusiveOf = "", validation = "")
var performanceLog: Option[File] = None
/** Input covariates table file for on-the-fly base quality score recalibration */
@Input(fullName = "BQSR", shortName = "BQSR", doc = "Input covariates table file for on-the-fly base quality score recalibration", required = false, exclusiveOf = "", validation = "")
var BQSR: File = _
var BQSR: Option[File] = _
/** Quantize quality scores to a given number of levels (with -BQSR) */
@Argument(fullName = "quantize_quals", shortName = "qq", doc = "Quantize quality scores to a given number of levels (with -BQSR)", required = false, exclusiveOf = "", validation = "")
var quantize_quals: Option[Int] = None
var quantize_quals: Option[Int] = config("quantize_quals")
/** Use static quantized quality scores to a given number of levels (with -BQSR) */
@Argument(fullName = "static_quantized_quals", shortName = "SQQ", doc = "Use static quantized quality scores to a given number of levels (with -BQSR)", required = false, exclusiveOf = "quantize_quals", validation = "")
var static_quantized_quals: Seq[Int] = Nil
var static_quantized_quals: List[Int] = config("static_quantized_quals", default = Nil)
/** Round quals down to nearest quantized qual */
@Argument(fullName = "round_down_quantized", shortName = "RDQ", doc = "Round quals down to nearest quantized qual", required = false, exclusiveOf = "quantize_quals", validation = "")
var round_down_quantized: Boolean = _
var round_down_quantized: Boolean = config("round_down_quantized", default = false)
/** Disable printing of base insertion and deletion tags (with -BQSR) */
@Argument(fullName = "disable_indel_quals", shortName = "DIQ", doc = "Disable printing of base insertion and deletion tags (with -BQSR)", required = false, exclusiveOf = "", validation = "")
var disable_indel_quals: Boolean = _
var disable_indel_quals: Boolean = config("disable_indel_quals", default = false)
/** Emit the OQ tag with the original base qualities (with -BQSR) */
@Argument(fullName = "emit_original_quals", shortName = "EOQ", doc = "Emit the OQ tag with the original base qualities (with -BQSR)", required = false, exclusiveOf = "", validation = "")
var emit_original_quals: Boolean = _
var emit_original_quals: Boolean = config("emit_original_quals", default = false)
/** Don't recalibrate bases with quality scores less than this threshold (with -BQSR) */
@Argument(fullName = "preserve_qscores_less_than", shortName = "preserveQ", doc = "Don't recalibrate bases with quality scores less than this threshold (with -BQSR)", required = false, exclusiveOf = "", validation = "")
var preserve_qscores_less_than: Option[Int] = None
var preserve_qscores_less_than: Option[Int] = config("preserve_qscores_less_than")
/** Global Qscore Bayesian prior to use for BQSR */
@Argument(fullName = "globalQScorePrior", shortName = "globalQScorePrior", doc = "Global Qscore Bayesian prior to use for BQSR", required = false, exclusiveOf = "", validation = "")
var globalQScorePrior: Option[Double] = None
var globalQScorePrior: Option[Double] = config("globalQScorePrior")
/** Format string for globalQScorePrior */
@Argument(fullName = "globalQScorePriorFormat", shortName = "", doc = "Format string for globalQScorePrior", required = false, exclusiveOf = "", validation = "")
......@@ -188,59 +188,59 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
/** How strict should we be with validation */
@Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false, exclusiveOf = "", validation = "")
var validation_strictness: htsjdk.samtools.ValidationStringency = _
var validation_strictness: Option[String] = config("validation_strictness")
/** Remove program records from the SAM header */
@Argument(fullName = "remove_program_records", shortName = "rpr", doc = "Remove program records from the SAM header", required = false, exclusiveOf = "", validation = "")
var remove_program_records: Boolean = _
var remove_program_records: Boolean = config("remove_program_records", default = false)
/** Keep program records in the SAM header */
@Argument(fullName = "keep_program_records", shortName = "kpr", doc = "Keep program records in the SAM header", required = false, exclusiveOf = "", validation = "")
var keep_program_records: Boolean = _
var keep_program_records: Boolean = config("keep_program_records", default = false)
/** Rename sample IDs on-the-fly at runtime using the provided mapping file */
@Argument(fullName = "sample_rename_mapping_file", shortName = "sample_rename_mapping_file", doc = "Rename sample IDs on-the-fly at runtime using the provided mapping file", required = false, exclusiveOf = "", validation = "")
var sample_rename_mapping_file: File = _
@Input(fullName = "sample_rename_mapping_file", shortName = "sample_rename_mapping_file", doc = "Rename sample IDs on-the-fly at runtime using the provided mapping file", required = false, exclusiveOf = "", validation = "")
var sample_rename_mapping_file: Option[File] = config("sample_rename_mapping_file")
/** Enable unsafe operations: nothing will be checked at runtime */
@Argument(fullName = "unsafe", shortName = "U", doc = "Enable unsafe operations: nothing will be checked at runtime", required = false, exclusiveOf = "", validation = "")
var unsafe: org.broadinstitute.gatk.utils.ValidationExclusion.TYPE = _
var unsafe: Option[String] = config("unsafe")
/** Disable both auto-generation of index files and index file locking */
@Argument(fullName = "disable_auto_index_creation_and_locking_when_reading_rods", shortName = "disable_auto_index_creation_and_locking_when_reading_rods", doc = "Disable both auto-generation of index files and index file locking", required = false, exclusiveOf = "", validation = "")
var disable_auto_index_creation_and_locking_when_reading_rods: Boolean = _
var disable_auto_index_creation_and_locking_when_reading_rods: Boolean = config("disable_auto_index_creation_and_locking_when_reading_rods", default = false)
/** Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests. */
@Argument(fullName = "no_cmdline_in_header", shortName = "no_cmdline_in_header", doc = "Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.", required = false, exclusiveOf = "", validation = "")
var no_cmdline_in_header: Boolean = _
var no_cmdline_in_header: Boolean = config("no_cmdline_in_header", default = false)
/** Just output sites without genotypes (i.e. only the first 8 columns of the VCF) */
@Argument(fullName = "sites_only", shortName = "sites_only", doc = "Just output sites without genotypes (i.e. only the first 8 columns of the VCF)", required = false, exclusiveOf = "", validation = "")
var sites_only: Boolean = _
var sites_only: Boolean = config("sites_only", default = false)
/** Always output all the records in VCF FORMAT fields, even if some are missing */
@Argument(fullName = "never_trim_vcf_format_field", shortName = "writeFullFormat", doc = "Always output all the records in VCF FORMAT fields, even if some are missing", required = false, exclusiveOf = "", validation = "")
var never_trim_vcf_format_field: Boolean = _
var never_trim_vcf_format_field: Boolean = config("never_trim_vcf_format_field", default = false)
/** Force BCF output, regardless of the file's extension */
@Argument(fullName = "bcf", shortName = "bcf", doc = "Force BCF output, regardless of the file's extension", required = false, exclusiveOf = "", validation = "")
var bcf: Boolean = _
var bcf: Boolean = config("bcf", default = false)
/** Compression level to use for writing BAM files (0 - 9, higher is more compressed) */
@Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files (0 - 9, higher is more compressed)", required = false, exclusiveOf = "", validation = "")
var bam_compression: Option[Int] = None
var bam_compression: Option[Int] = config("bam_compression")
/** If provided, output BAM/CRAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier */
@Argument(fullName = "simplifyBAM", shortName = "simplifyBAM", doc = "If provided, output BAM/CRAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier", required = false, exclusiveOf = "", validation = "")
var simplifyBAM: Boolean = _
var simplifyBAM: Boolean = config("simplifyBAM", default = false)
/** Turn off on-the-fly creation of indices for output BAM/CRAM files. */
@Argument(fullName = "disable_bam_indexing", shortName = "", doc = "Turn off on-the-fly creation of indices for output BAM/CRAM files.", required = false, exclusiveOf = "", validation = "")
var disable_bam_indexing: Boolean = _
var disable_bam_indexing: Boolean = config("disable_bam_indexing", default = false)
/** Enable on-the-fly creation of md5s for output BAM files. */
@Argument(fullName = "generate_md5", shortName = "", doc = "Enable on-the-fly creation of md5s for output BAM files.", required = false, exclusiveOf = "", validation = "")
var generate_md5: Boolean = _
var generate_md5: Boolean = config("generate_md5", default = false)
/** Number of data threads to allocate to this analysis */
@Argument(fullName = "num_threads", shortName = "nt", doc = "Number of data threads to allocate to this analysis", required = false, exclusiveOf = "", validation = "")
......@@ -256,7 +256,7 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
/** Enable threading efficiency monitoring */
@Argument(fullName = "monitorThreadEfficiency", shortName = "mte", doc = "Enable threading efficiency monitoring", required = false, exclusiveOf = "", validation = "")
var monitorThreadEfficiency: Boolean = _
var monitorThreadEfficiency: Boolean = config("monitorThreadEfficiency", default = false)
/** When using IO threads, total number of BAM file handles to keep open simultaneously */
@Argument(fullName = "num_bam_file_handles", shortName = "bfh", doc = "When using IO threads, total number of BAM file handles to keep open simultaneously", required = false, exclusiveOf = "", validation = "")
......@@ -264,57 +264,49 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
/** Exclude read groups based on tags */
@Input(fullName = "read_group_black_list", shortName = "rgbl", doc = "Exclude read groups based on tags", required = false, exclusiveOf = "", validation = "")
var read_group_black_list: Seq[File] = Nil
var read_group_black_list: List[File] = config("read_group_black_list", default = Nil)
/** Pedigree files for samples */
@Argument(fullName = "pedigree", shortName = "ped", doc = "Pedigree files for samples", required = false, exclusiveOf = "", validation = "")
var pedigree: Seq[File] = Nil
var pedigree: List[File] = config("pedigree", default = Nil)
/** Pedigree string for samples */
@Argument(fullName = "pedigreeString", shortName = "pedString", doc = "Pedigree string for samples", required = false, exclusiveOf = "", validation = "")
var pedigreeString: Seq[String] = Nil
var pedigreeString: List[String] = config("pedigreeString", default = Nil)
/** Validation strictness for pedigree information */
@Argument(fullName = "pedigreeValidationType", shortName = "pedValidationType", doc = "Validation strictness for pedigree information", required = false, exclusiveOf = "", validation = "")
var pedigreeValidationType: org.broadinstitute.gatk.engine.samples.PedigreeValidationType = _
var pedigreeValidationType: Option[String] = config("pedigreeValidationType")
/** Allow interval processing with an unsupported BAM/CRAM */
@Argument(fullName = "allow_intervals_with_unindexed_bam", shortName = "", doc = "Allow interval processing with an unsupported BAM/CRAM", required = false, exclusiveOf = "", validation = "")
var allow_intervals_with_unindexed_bam: Boolean = _
var allow_intervals_with_unindexed_bam: Boolean = config("allow_intervals_with_unindexed_bam", default = false)
/** Write a BCF copy of the output VCF */
@Argument(fullName = "generateShadowBCF", shortName = "generateShadowBCF", doc = "Write a BCF copy of the output VCF", required = false, exclusiveOf = "", validation = "")
var generateShadowBCF: Boolean = _
var generateShadowBCF: Boolean = config("generateShadowBCF", default = false)
/** Type of IndexCreator to use for VCF/BCF indices */
@Argument(fullName = "variant_index_type", shortName = "variant_index_type", doc = "Type of IndexCreator to use for VCF/BCF indices", required = false, exclusiveOf = "", validation = "")
var variant_index_type: org.broadinstitute.gatk.utils.variant.GATKVCFIndexType = _
var variant_index_type: Option[String] = config("variant_index_type")
/** Parameter to pass to the VCF/BCF IndexCreator */
@Argument(fullName = "variant_index_parameter", shortName = "variant_index_parameter", doc = "Parameter to pass to the VCF/BCF IndexCreator", required = false, exclusiveOf = "", validation = "")
var variant_index_parameter: Option[Int] = None
var variant_index_parameter: Option[Int] = config("variant_index_parameter")
/** Reference window stop */
@Argument(fullName = "reference_window_stop", shortName = "ref_win_stop", doc = "Reference window stop", required = false, exclusiveOf = "", validation = "")
var reference_window_stop: Option[Int] = None
var reference_window_stop: Option[Int] = config("reference_window_stop")
/** Set the minimum level of logging */
@Argument(fullName = "logging_level", shortName = "l", doc = "Set the minimum level of logging", required = false, exclusiveOf = "", validation = "")
var logging_level: String = _
var logging_level: Option[String] = config("logging_level")
/** Set the logging location */
@Output(fullName = "log_to_file", shortName = "log", doc = "Set the logging location", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
var log_to_file: File = _
/** Generate the help message */
@Argument(fullName = "help", shortName = "h", doc = "Generate the help message", required = false, exclusiveOf = "", validation = "")
var help: Boolean = _
/** Output version information */
@Argument(fullName = "version", shortName = "version", doc = "Output version information", required = false, exclusiveOf = "", validation = "")
var version: Boolean = _
def versionRegex = """(.*)""".r
override def versionExitcode = List(0, 1)
def versionCommand = executable + " -jar " + jarFile + " -version"
......@@ -399,7 +391,5 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
optional("-variant_index_parameter", variant_index_parameter, spaceSeparated = true, escape = true, format = "%s") +
optional("-ref_win_stop", reference_window_stop, spaceSeparated = true, escape = true, format = "%s") +
optional("-l", logging_level, spaceSeparated = true, escape = true, format = "%s") +
optional("-log", log_to_file, spaceSeparated = true, escape = true, format = "%s") +
conditional(help, "-h", escape = true, format = "%s") +
conditional(version, "-version", escape = true, format = "%s")
optional("-log", log_to_file, spaceSeparated = true, escape = true, format = "%s")
}
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