Commit c2ef1e2e authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'fix-small_fixes' into 'develop'

Fix small fixes



See merge request !357
parents c3e36d0c 8a6f4376
......@@ -20,6 +20,14 @@
* Added trimming of reverse complement adapters (flexiprep does this automatic)
* Added [Tinycap](../pipelines/tinycap.md) for smallRNA analysis
* [Gentrap](../pipelines/gentrap.md): Refactoring changed the "expression_measures" options
* Fixed biopet logging
* Added sample tagging
* Seqstat now reports histogram of read lengths
* Fixed bug in seqstat when having multiple sizes exists in the fastq file
* Added variant plots for targets to report of Shiva
* Adapter feed to cutadapt now use only that parts that are reported by fastqc and not the full sequence
* Added a reference selector when fasta file can't be found. User now get a list of available species and genomes in the config
* Fixed bcftools with IUPAC symbols
## Infrastructure changes
......
......@@ -38,89 +38,89 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
var outputVcf: File = null
@Input(required = false)
var bam_list: Option[File] = config("bam_list")
var bamList: Option[File] = config("bam_list")
@Input(required = false)
var targets: Option[File] = config("targets")
var targets: Option[File] = config("targets", freeVar = false)
@Input(required = false)
var samples: Option[File] = config("samples")
var samples: Option[File] = config("samples", freeVar = false)
@Input(required = false)
var populations: Option[File] = config("populations")
var populations: Option[File] = config("populations", freeVar = false)
@Input(required = false)
var cnv_map: Option[File] = config("cnv_map")
var cnvMap: Option[File] = config("cnv_map", freeVar = false)
@Input(required = false)
var trace: Option[File] = config("trace")
var trace: Option[File] = config("trace", freeVar = false)
@Input(required = false)
var failed_alleles: Option[File] = config("failed_alleles")
var failedAlleles: Option[File] = config("failed_alleles", freeVar = false)
@Input(required = false)
var observation_bias: Option[File] = config("observation_bias")
var observationBias: Option[File] = config("observation_bias")
@Input(required = false)
var contamination_estimates: Option[File] = config("contamination_estimates")
var contaminationEstimates: Option[File] = config("contamination_estimates")
@Input(required = false)
var variant_input: Option[File] = config("variant_input")
var variantInput: Option[File] = config("variant_input", freeVar = false)
@Input(required = false)
var haplotype_basis_alleles: Option[File] = config("haplotype_basis_alleles")
var pvar: Option[Int] = config("pvar")
var theta: Option[Int] = config("theta")
var ploidy: Option[Int] = config("ploidy")
var use_best_n_alleles: Option[Int] = config("use_best_n_alleles")
var max_complex_gap: Option[Int] = config("max_complex_gap")
var min_repeat_size: Option[Int] = config("min_repeat_size")
var min_repeat_entropy: Option[Int] = config("min_repeat_entropy")
var read_mismatch_limit: Option[Int] = config("read_mismatch_limit")
var read_max_mismatch_fraction: Option[Int] = config("read_max_mismatch_fraction")
var read_snp_limit: Option[Int] = config("read_snp_limit")
var read_indel_limit: Option[Int] = config("read_indel_limit")
var min_alternate_fraction: Option[Double] = config("min_alternate_fraction")
var min_alternate_count: Option[Int] = config("min_alternate_count")
var min_alternate_qsum: Option[Int] = config("min_alternate_qsum")
var min_alternate_total: Option[Int] = config("min_alternate_total")
var min_coverage: Option[Int] = config("min_coverage")
var genotyping_max_iterations: Option[Int] = config("genotyping_max_iterations")
var genotyping_max_banddepth: Option[Int] = config("genotyping_max_banddepth")
var genotype_variant_threshold: Option[Int] = config("genotype_variant_threshold")
var read_dependence_factor: Option[Int] = config("read_dependence_factor")
var min_mapping_quality: Option[Double] = config("min_mapping_quality")
var min_base_quality: Option[Double] = config("min_base_quality")
var min_supporting_allele_qsum: Option[Double] = config("min_supporting_allele_qsum")
var min_supporting_mapping_qsum: Option[Double] = config("min_supporting_mapping_qsum")
var mismatch_base_quality_threshold: Option[Double] = config("mismatch_base_quality_threshold")
var base_quality_cap: Option[Double] = config("base_quality_cap")
var prob_contamination: Option[Double] = config("prob_contamination")
var only_use_input_alleles: Boolean = config("only_use_input_alleles", default = false)
var report_all_haplotype_alleles: Boolean = config("report_all_haplotype_alleles", default = false)
var report_monomorphic: Boolean = config("report_monomorphic", default = false)
var pooled_discrete: Boolean = config("pooled_discrete", default = false)
var pooled_continuous: Boolean = config("pooled_continuous", default = false)
var use_reference_allele: Boolean = config("use_reference_allele", default = false)
var no_snps: Boolean = config("no_snps", default = false)
var no_indels: Boolean = config("no_indels", default = false)
var no_mnps: Boolean = config("no_mnps", default = false)
var no_complex: Boolean = config("no_complex", default = false)
var no_partial_observations: Boolean = config("no_partial_observations", default = false)
var dont_left_align_indels: Boolean = config("dont_left_align_indels", default = false)
var use_duplicate_reads: Boolean = config("use_duplicate_reads", default = false)
var standard_filters: Boolean = config("standard_filters", default = false)
var no_population_priors: Boolean = config("no_population_priors", default = false)
var hwe_priors_off: Boolean = config("hwe_priors_off", default = false)
var binomial_obs_priors_off: Boolean = config("binomial_obs_priors_off", default = false)
var allele_balance_priors_off: Boolean = config("allele_balance_priors_off", default = false)
var legacy_gls: Boolean = config("legacy_gls", default = false)
var report_genotype_likelihood_max: Boolean = config("report_genotype_likelihood_max", default = false)
var exclude_unobserved_genotypes: Boolean = config("exclude_unobserved_genotypes", default = false)
var use_mapping_quality: Boolean = config("use_mapping_quality", default = false)
var harmonic_indel_quality: Boolean = config("harmonic_indel_quality", default = false)
var genotype_qualities: Boolean = config("genotype_qualities", default = false)
var haplotypeBasisAlleles: Option[File] = config("haplotype_basis_alleles", freeVar = false)
var pvar: Option[Int] = config("pvar", freeVar = false)
var theta: Option[Int] = config("theta", freeVar = false)
var ploidy: Option[Int] = config("ploidy", freeVar = false)
var useBestNAlleles: Option[Int] = config("use_best_n_alleles")
var maxComplexGap: Option[Int] = config("max_complex_gap")
var minRepeatSize: Option[Int] = config("min_repeat_size")
var minRepeatEntropy: Option[Int] = config("min_repeat_entropy")
var readMismatchLimit: Option[Int] = config("read_mismatch_limit")
var readMaxMismatchFraction: Option[Int] = config("read_max_mismatch_fraction")
var readSnpLimit: Option[Int] = config("read_snp_limit")
var readIndelLimit: Option[Int] = config("read_indel_limit")
var minAlternateFraction: Option[Double] = config("min_alternate_fraction")
var minAlternateCount: Option[Int] = config("min_alternate_count")
var minAlternateQsum: Option[Int] = config("min_alternate_qsum")
var minAlternateTotal: Option[Int] = config("min_alternate_total")
var minCoverage: Option[Int] = config("min_coverage")
var genotypingMaxIterations: Option[Int] = config("genotyping_max_iterations")
var genotypingMaxBanddepth: Option[Int] = config("genotyping_max_banddepth")
var genotypeVariantThreshold: Option[Int] = config("genotype_variant_threshold")
var readDependenceFactor: Option[Int] = config("read_dependence_factor")
var minMappingQuality: Option[Double] = config("min_mapping_quality")
var minBaseQuality: Option[Double] = config("min_base_quality")
var minSupportingAlleleQsum: Option[Double] = config("min_supporting_allele_qsum")
var minSupportingMappingQsum: Option[Double] = config("min_supporting_mapping_qsum")
var mismatchBaseQualityThreshold: Option[Double] = config("mismatch_base_quality_threshold")
var baseQualityCap: Option[Double] = config("base_quality_cap")
var probContamination: Option[Double] = config("prob_contamination")
var onlyUseInputAlleles: Boolean = config("only_use_input_alleles", default = false)
var reportAllHaplotypeAlleles: Boolean = config("report_all_haplotype_alleles", default = false)
var reportMonomorphic: Boolean = config("report_monomorphic", default = false)
var pooledDiscrete: Boolean = config("pooled_discrete", default = false)
var pooledContinuous: Boolean = config("pooled_continuous", default = false)
var useReferenceAllele: Boolean = config("use_reference_allele", default = false)
var noSnps: Boolean = config("no_snps", default = false)
var noIndels: Boolean = config("no_indels", default = false)
var noMnps: Boolean = config("no_mnps", default = false)
var noComplex: Boolean = config("no_complex", default = false)
var noPartialObservations: Boolean = config("no_partial_observations", default = false)
var dontLeftAlignIndels: Boolean = config("dont_left_align_indels", default = false)
var useDuplicateReads: Boolean = config("use_duplicate_reads", default = false)
var standardFilters: Boolean = config("standard_filters", default = false)
var noPopulationPriors: Boolean = config("no_population_priors", default = false)
var hwePriorsOff: Boolean = config("hwe_priors_off", default = false)
var binomialObsPriorsOff: Boolean = config("binomial_obs_priors_off", default = false)
var alleleBalancePriorsOff: Boolean = config("allele_balance_priors_off", default = false)
var legacyGls: Boolean = config("legacy_gls", default = false)
var reportGenotypeLikelihoodMax: Boolean = config("report_genotype_likelihood_max", default = false)
var excludeUnobservedGenotypes: Boolean = config("exclude_unobserved_genotypes", default = false)
var useMappingQuality: Boolean = config("use_mapping_quality", default = false)
var harmonicIndelQuality: Boolean = config("harmonic_indel_quality", default = false)
var genotypeQualities: Boolean = config("genotype_qualities", default = false)
var debug: Boolean = config("debug", default = logger.isDebugEnabled)
var haplotypeLength: Option[Int] = config("haplotype_length")
......@@ -137,68 +137,68 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
def cmdLine = executable +
required("--fasta-reference", reference) +
repeat("--bam", bamfiles) +
optional("--bam-list", bam_list) +
optional("--bam-list", bamList) +
optional("--targets", targets) +
optional("--samples", samples) +
optional("--populations", populations) +
optional("--cnv-map", cnv_map) +
optional("--cnv-map", cnvMap) +
optional("--trace", trace) +
optional("--failed-alleles", failed_alleles) +
optional("--observation-bias", observation_bias) +
optional("--contamination-estimates", contamination_estimates) +
optional("--variant-input", variant_input) +
optional("--haplotype-basis-alleles", haplotype_basis_alleles) +
optional("--failed-alleles", failedAlleles) +
optional("--observation-bias", observationBias) +
optional("--contamination-estimates", contaminationEstimates) +
optional("--variant-input", variantInput) +
optional("--haplotype-basis-alleles", haplotypeBasisAlleles) +
optional("--pvar", pvar) +
optional("--theta", theta) +
optional("--ploidy", ploidy) +
optional("--use-best-n-alleles", use_best_n_alleles) +
optional("--max-complex-gap", max_complex_gap) +
optional("--min-repeat-size", min_repeat_size) +
optional("--min-repeat-entropy", min_repeat_entropy) +
optional("--read-mismatch-limit", read_mismatch_limit) +
optional("--read-max-mismatch-fraction", read_max_mismatch_fraction) +
optional("--read-snp-limit", read_snp_limit) +
optional("--read-indel-limit", read_indel_limit) +
optional("--min-alternate-fraction", min_alternate_fraction) +
optional("--min-alternate-count", min_alternate_count) +
optional("--min-alternate-qsum", min_alternate_qsum) +
optional("--min-alternate-total", min_alternate_total) +
optional("--min-coverage", min_coverage) +
optional("--genotyping-max-iterations", genotyping_max_iterations) +
optional("--genotyping-max-banddepth", genotyping_max_banddepth) +
optional("--genotype-variant-threshold", genotype_variant_threshold) +
optional("--read-dependence-factor", read_dependence_factor) +
optional("--min-mapping-quality", min_mapping_quality) +
optional("--min-base-quality", min_base_quality) +
optional("--min-supporting-allele-qsum", min_supporting_allele_qsum) +
optional("--min-supporting-mapping-qsum", min_supporting_mapping_qsum) +
optional("--mismatch-base-quality-threshold", mismatch_base_quality_threshold) +
optional("--base-quality-cap", base_quality_cap) +
optional("--prob-contamination", prob_contamination) +
conditional(only_use_input_alleles, "--only-use-input-alleles") +
conditional(report_all_haplotype_alleles, "--report-all-haplotype-alleles") +
conditional(report_monomorphic, "--report-monomorphic") +
conditional(pooled_discrete, "--pooled-discrete") +
conditional(pooled_continuous, "--pooled-continuous") +
conditional(use_reference_allele, "--use-reference-allele") +
conditional(no_snps, "--no-snps") +
conditional(no_indels, "--no-indels") +
conditional(no_mnps, "--no-mnps") +
conditional(no_complex, "--no-complex") +
conditional(no_partial_observations, "--no-partial-observations") +
conditional(dont_left_align_indels, "--dont-left-align-indels") +
conditional(use_duplicate_reads, "--use-duplicate-reads") +
conditional(standard_filters, "--standard-filters") +
conditional(no_population_priors, "--no-population-priors") +
conditional(hwe_priors_off, "--hwe-priors-off") +
conditional(binomial_obs_priors_off, "--binomial-obs-priors-off") +
conditional(allele_balance_priors_off, "--allele-balance-priors-off") +
conditional(legacy_gls, "--legacy-gls") +
conditional(report_genotype_likelihood_max, "--report-genotype-likelihood-max") +
conditional(exclude_unobserved_genotypes, "--exclude-unobserved-genotypes") +
conditional(use_mapping_quality, "--use-mapping-quality") +
conditional(harmonic_indel_quality, "--harmonic-indel-quality") +
conditional(genotype_qualities, "--genotype-qualities") +
optional("--use-best-n-alleles", useBestNAlleles) +
optional("--max-complex-gap", maxComplexGap) +
optional("--min-repeat-size", minRepeatSize) +
optional("--min-repeat-entropy", minRepeatEntropy) +
optional("--read-mismatch-limit", readMismatchLimit) +
optional("--read-max-mismatch-fraction", readMaxMismatchFraction) +
optional("--read-snp-limit", readSnpLimit) +
optional("--read-indel-limit", readIndelLimit) +
optional("--min-alternate-fraction", minAlternateFraction) +
optional("--min-alternate-count", minAlternateCount) +
optional("--min-alternate-qsum", minAlternateQsum) +
optional("--min-alternate-total", minAlternateTotal) +
optional("--min-coverage", minCoverage) +
optional("--genotyping-max-iterations", genotypingMaxIterations) +
optional("--genotyping-max-banddepth", genotypingMaxBanddepth) +
optional("--genotype-variant-threshold", genotypeVariantThreshold) +
optional("--read-dependence-factor", readDependenceFactor) +
optional("--min-mapping-quality", minMappingQuality) +
optional("--min-base-quality", minBaseQuality) +
optional("--min-supporting-allele-qsum", minSupportingAlleleQsum) +
optional("--min-supporting-mapping-qsum", minSupportingMappingQsum) +
optional("--mismatch-base-quality-threshold", mismatchBaseQualityThreshold) +
optional("--base-quality-cap", baseQualityCap) +
optional("--prob-contamination", probContamination) +
conditional(onlyUseInputAlleles, "--only-use-input-alleles") +
conditional(reportAllHaplotypeAlleles, "--report-all-haplotype-alleles") +
conditional(reportMonomorphic, "--report-monomorphic") +
conditional(pooledDiscrete, "--pooled-discrete") +
conditional(pooledContinuous, "--pooled-continuous") +
conditional(useReferenceAllele, "--use-reference-allele") +
conditional(noSnps, "--no-snps") +
conditional(noIndels, "--no-indels") +
conditional(noMnps, "--no-mnps") +
conditional(noComplex, "--no-complex") +
conditional(noPartialObservations, "--no-partial-observations") +
conditional(dontLeftAlignIndels, "--dont-left-align-indels") +
conditional(useDuplicateReads, "--use-duplicate-reads") +
conditional(standardFilters, "--standard-filters") +
conditional(noPopulationPriors, "--no-population-priors") +
conditional(hwePriorsOff, "--hwe-priors-off") +
conditional(binomialObsPriorsOff, "--binomial-obs-priors-off") +
conditional(alleleBalancePriorsOff, "--allele-balance-priors-off") +
conditional(legacyGls, "--legacy-gls") +
conditional(reportGenotypeLikelihoodMax, "--report-genotype-likelihood-max") +
conditional(excludeUnobservedGenotypes, "--exclude-unobserved-genotypes") +
conditional(useMappingQuality, "--use-mapping-quality") +
conditional(harmonicIndelQuality, "--harmonic-indel-quality") +
conditional(genotypeQualities, "--genotype-qualities") +
conditional(debug, "--debug") +
optional("--haplotype-length", haplotypeLength) +
(if (inputAsStdin) required("--stdin") else "") +
......
......@@ -22,30 +22,31 @@ object BiopetToolsExecutable extends BiopetExecutable {
def pipelines: List[MainCommand] = Nil
def tools: List[MainCommand] = List(
nl.lumc.sasc.biopet.tools.MergeTables,
nl.lumc.sasc.biopet.tools.WipeReads,
nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
nl.lumc.sasc.biopet.tools.FastqSync,
nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
nl.lumc.sasc.biopet.tools.BaseCounter,
nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
nl.lumc.sasc.biopet.tools.BiopetFlagstat,
nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
nl.lumc.sasc.biopet.tools.VcfToTsv,
nl.lumc.sasc.biopet.tools.VcfFilter,
nl.lumc.sasc.biopet.tools.VcfStats,
nl.lumc.sasc.biopet.tools.BaseCounter,
nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
nl.lumc.sasc.biopet.tools.FastqSplitter,
nl.lumc.sasc.biopet.tools.FastqSync,
nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
nl.lumc.sasc.biopet.tools.GvcfToBed,
nl.lumc.sasc.biopet.tools.MergeAlleles,
nl.lumc.sasc.biopet.tools.MergeTables,
nl.lumc.sasc.biopet.tools.MpileupToVcf,
nl.lumc.sasc.biopet.tools.FastqSplitter,
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
nl.lumc.sasc.biopet.tools.PrefixFastq,
nl.lumc.sasc.biopet.tools.SageCountFastq,
nl.lumc.sasc.biopet.tools.SageCreateLibrary,
nl.lumc.sasc.biopet.tools.SageCreateTagCounts,
nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
nl.lumc.sasc.biopet.tools.MergeAlleles,
nl.lumc.sasc.biopet.tools.SamplesTsvToJson,
nl.lumc.sasc.biopet.tools.SeqStat,
nl.lumc.sasc.biopet.tools.VepNormalizer,
nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
nl.lumc.sasc.biopet.tools.VcfWithVcf,
nl.lumc.sasc.biopet.tools.SquishBed,
nl.lumc.sasc.biopet.tools.SummaryToTsv,
nl.lumc.sasc.biopet.tools.ValidateFastq,
nl.lumc.sasc.biopet.tools.KrakenReportToJson)
nl.lumc.sasc.biopet.tools.VcfFilter,
nl.lumc.sasc.biopet.tools.VcfStats,
nl.lumc.sasc.biopet.tools.VcfToTsv,
nl.lumc.sasc.biopet.tools.VcfWithVcf,
nl.lumc.sasc.biopet.tools.VepNormalizer,
nl.lumc.sasc.biopet.tools.WipeReads)
}
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