etc/gatk-wdl/fm2/fm2.wdl

   1 version 1.0
   2
   3 import "tasks/sample.wdl" as sampleWf
   4 import "tasks/common.wdl" as common
   5 import "tasks/structs.wdl" as structs
   6
   7 workflow fm2 {
   8         input {
   9                 File sampleConfigFile
  10                 String outputDir = "."
  11                 String platform = "illumina"
  12                 Boolean useBwaKit = false
  13                 Int scatterSizeMillions = 1000
  14                 Int? minBWAmatchLen = 200
  15                 BwaIndex bwaIndex
  16                 GatkIndex GatkIndex
  17                 String? adapterForward = "AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA"  # Illumina universal adapter.
  18                 String? adapterReverse = "AAGTCGGATCGTAGCCATGTCGTTC"  # Illumina universal adapter.
  19                 Int? scatterSize
  20                 Int bwaThreads = 4
  21                 File dockerImagesFile
  22         }
  23
  24         # Parse docker Tags configuration and sample sheet.
  25         call common.YamlToJson as convertDockerImagesFile {
  26                 input:
  27                         yaml = dockerImagesFile,
  28                         outputJson = "dockerImages.json"
  29         }
  30
  31         Map[String, String] dockerImages = read_json(convertDockerImagesFile.json)
  32         #Array[Array[File]] inputSamples = read_tsv(SampleFqTSV)
  33         SampleConfig sampleConfig = read_json(sampleConfigFile)
  34
  35         scatter (sample in sampleConfig.samples) {
  36                 String sampleIds = sample.id
  37                 String sampleDir = outputDir + "/samples/" + sample.id + "/"
  38                 call sampleWf.SampleWorkflow as sampleWorkflow {
  39                         input:
  40                                 sampleDir = sampleDir,
  41                                 sample = sample,
  42                                 bwaThreads = bwaThreads,
  43                                 bwaIndex = bwaIndex,
  44                                 #bwaMem2Index = bwaMem2Index,
  45                                 GatkIndex = GatkIndex,
  46                                 adapterForward = adapterForward,
  47                                 adapterReverse = adapterReverse,
  48                                 useBwaKit = useBwaKit,
  49                                 dockerImages = dockerImages,
  50                                 #scatters = scatterList.scatters,
  51                                 bwaThreads = bwaThreads,
  52                                 platform = platform,
  53                                 minBWAmatchLen = minBWAmatchLen
  54                                 #sampleName = sample.id,
  55                                 #gender = select_first([sample.gender, "unknown"]),
  56                 }
  57         }
  58
  59         Array[File] allReports = flatten([
  60                 flatten(sampleWorkflow.reports)
  61                 #, flatten(singleSampleCalling.reports)
  62         ])
  63
  64         output {
  65                 File dockerImagesList = convertDockerImagesFile.json
  66                 #File multiqcReport = multiqcTask.multiqcReport
  67                 Array[File] reports = allReports
  68                 #Array[File] recalibratedBams = sampleWorkflow.recalibratedBam
  69                 #Array[File] recalibratedBamIndexes = sampleWorkflow.recalibratedBamIndex
  70                 Array[File] markdupBams = sampleWorkflow.markdupBam
  71                 Array[File] markdupBamIndexes = sampleWorkflow.markdupBamIndex
  72                 Array[File] filteredBam = sampleWorkflow.filteredBam
  73                 Array[File] filteredBamIndex = sampleWorkflow.filteredBamIndex
  74                 Array[File] outSNP0txts = sampleWorkflow.outSNP0txt
  75                 Array[File] outSTR0txts = sampleWorkflow.outSTR0txt
  76                 Array[File] outSNP1txts = sampleWorkflow.outSNP1txt
  77                 Array[File] outSNPtxts = sampleWorkflow.outSNPtxt
  78                 Array[File] outSTRtxts = sampleWorkflow.outSTRtxt
  79                 Array[File] outbcfFiles = sampleWorkflow.outbcfFile
  80                 Array[File] outsnpFiles = sampleWorkflow.outsnpFile
  81                 Array[File] outsnpIndexFiles = sampleWorkflow.outsnpIndexFile
  82                 Array[File] outsnp0Files = sampleWorkflow.outsnp0File
  83                 Array[File] outsnp0IndexFiles = sampleWorkflow.outsnp0IndexFile
  84                 #Array[File?] mantaVCFs = svCalling.mantaVcf
  85                 #Array[File?] dellyVCFs = svCalling.dellyVcf
  86                 #Array[File?] survivorVCFs = svCalling.survivorVcf
  87                 #Array[Array[File]?] modifiedVcfs = svCalling.modifiedVcfs
  88         }
  89
  90         parameter_meta {
  91                 # inputs
  92                 sampleConfigFile: {description: "The samplesheet, including sample ids, library ids, readgroup ids and fastq file locations.", category: "required"}
  93                 outputDir: {description: "The directory the output should be written to.", category: "common"}
  94                 platform: {description: "The platform used for sequencing.", category: "advanced"}
  95                 useBwaKit: {description: "Whether or not BWA kit should be used. If false BWA mem will be used.", category: "advanced"}
  96                 scatterSizeMillions:{description: "Same as scatterSize, but is multiplied by 1000000 to get scatterSize. This allows for setting larger values more easily.", category: "advanced"}
  97                 bwaIndex: {description: "The BWA index files. When these are provided BWA will be used.", category: "common"}
  98                 adapterForward: {description: "The adapter to be removed from the reads first or single end reads.", category: "common"}
  99                 adapterReverse: {description: "The adapter to be removed from the reads second end reads.", category: "common"}
 100                 scatterSize: {description: "The size of the scattered regions in bases for the GATK subworkflows. Scattering is used to speed up certain processes. The genome will be seperated into multiple chunks (scatters) which will be processed in their own job, allowing for parallel processing. Higher values will result in a lower number of jobs. The optimal value here will depend on the available resources.", category: "advanced"}
 101                 bwaThreads: {description: "The amount of threads for the alignment process.", category: "advanced"}
 102                 dockerImagesFile: {description: "A YAML file describing the docker image used for the tasks. The dockerImages.yml provided with the pipeline is recommended.", category: "advanced"}
 103
 104                 # outputs
 105                 dockerImagesList: {description: "Json file describing the docker images used by the pipeline."}
 106                 reports: {description: ""}
 107                 recalibratedBams: {description: ""}
 108                 recalibratedBamIndexes: {description: ""}
 109                 markdupBams: {description: ""}
 110                 markdupBamIndexes: {description: ""}
 111         }
 112 }