Bestie/structs.wdl at develop · mmterpstra/Bestie · GitHub

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version 1.0

struct IndexedFile {
    File file
    File index
}
struct ReadGroup {
    #should be unique for multiple samples??
    String identifier
    File fastq1
    File? fastq2
    File? fastqUmi

    #docs for read structures: https://fulcrumgenomics.github.io/fgbio/tools/1.5.1/ExtractUmisFromBam.html
    # Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
    #    T identifies a template read
    #    B identifies a sample barcode read
    #    M identifies a unique molecular index read
    #    S identifies a set of bases that should be skipped or ignored

    String? readStructureFastq1
    #default +T
    String? readStructureFastq2
    #default +M
    String? readStructureFastqUmi
    Boolean? extractUmisFromReadNames

    #usually assume library is approximated by sample_barcode1(+barcode2) if not here is your parameter to overwrite
    String? library
    #[ATCGN]{6+}
    String barcode1
    String? barcode2
    #001 or something
    String? run
    #HXXXXXXXX or something
    String? flowcell
    #L000
    String? lane
    #YYYYMMDD
    String? date
    #hiseq/miseq etc
    String? sequencer
    #illumina
    String? platform
    #
    String? platform_model
    #
    String? sequencing_center
}

struct SampleDescriptor {
    String name
    #for smRNA mirDeep2 compatibility
    String? threeLetterName
    #for designating as tumor: if the normal string is present then it is a tumor sample and the normal is linked normal sample name
    String? normal
    String? gender
    Boolean? runTwistUmi
    IndexedFile? alignedReads
    Array[ReadGroup] readgroups
}


struct SampleConfig {
    Array[SampleDescriptor] samples
    IndexedFile? genomicVariants
    IndexedFile? somaticVariants
}
#wip maybe in future analysis workflows
struct TumorNormalSampleConfig {
    #This should be treated as a single patient config maybe better parameterisation to be added
    Array[SampleDescriptor] panelNormals
    Array[SampleDescriptor] normals
    Array[SampleDescriptor] tumors
}

struct BwaIndex {
    File fastaFile
    File ambFile
    File annFile
    File bwtFile
    File pacFile
    File saFile
    #placeholder for optional alt stuff
    File? altFile
}

struct Reference {
    File fasta
    File dict
    File fai
}