etc/gatk-wdl/fm2/tasks/sample.wdl

   1 version 1.0
   2
   3 # Copyright (c) 2018 Leiden University Medical Center
   4 #
   5 # Permission is hereby granted, free of charge, to any person obtaining a copy
   6 # of this software and associated documentation files (the "Software"), to deal
   7 # in the Software without restriction, including without limitation the rights
   8 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   9 # copies of the Software, and to permit persons to whom the Software is
  10 # furnished to do so, subject to the following conditions:
  11 #
  12 # The above copyright notice and this permission notice shall be included in
  13 # all copies or substantial portions of the Software.
  14 #
  15 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  16 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  17 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  18 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  19 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  20 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  21 # SOFTWARE.
  22
  23 #import "BamMetrics/bammetrics.wdl" as bammetrics
  24 #import "gatk-preprocess/gatk-preprocess.wdl" as preprocess
  25 import "structs.wdl" as structs
  26 import "bwa.wdl" as bwa
  27 import "fgi.wdl" as fgifm2
  28 import "sambamba.wdl" as sambamba
  29 #import "tasks/picard.wdl" as picard
  30 import "QC.wdl" as qc
  31 #import "tasks/umi-tools.wdl" as umiTools
  32
  33 workflow SampleWorkflow {
  34         input {
  35                 Sample sample
  36                 String sampleDir
  37                 String platform = "illumina"
  38                 Boolean useBwaKit = false
  39
  40                 BwaIndex bwaIndex
  41                 GatkIndex GatkIndex
  42                 String? adapterForward
  43                 String? adapterReverse
  44                 Int? minBWAmatchLen = 200
  45
  46                 Int bwaThreads = 4
  47                 Map[String, String] dockerImages
  48         }
  49
  50         scatter (readgroup in sample.readgroups) {
  51                 String readgroupDir = sampleDir + "/lib_" + readgroup.lib_id + "--rg_" + readgroup.id
  52                 call qc.QC as qualityControl {
  53                         input:
  54                                 outputDir = readgroupDir,
  55                                 read1 = readgroup.R1,
  56                                 read2 = readgroup.R2,
  57                                 adapterForward = adapterForward,
  58                                 adapterReverse = adapterReverse,
  59                 }
  60                 call bwa.Mem as bwaMem {
  61                         input:
  62                                 read1 = qualityControl.qcRead1,
  63                                 read2 = qualityControl.qcRead2,
  64                                 outputPrefix = readgroupDir + "/" + sample.id + "-" + readgroup.lib_id + "-" + readgroup.id,
  65                                 readgroup = "@RG\\tID:~{sample.id}-~{readgroup.lib_id}-~{readgroup.id}\\tLB:~{readgroup.lib_id}\\tSM:~{sample.id}\\tPL:~{platform}",
  66                                 bwaIndex = select_first([bwaIndex]),
  67                                 threads = bwaThreads,
  68                                 usePostalt = useBwaKit,
  69                                 dockerImage = dockerImages["bwakit+samtools"]
  70                 }
  71                 Boolean paired = defined(readgroup.R2)
  72
  73         }
  74         call sambamba.Markdup as markdup {
  75                 input:
  76                         inputBams = select_all(bwaMem.outputBam),
  77                         outputPath = sampleDir + "/" + sample.id + ".markdup.bam",
  78                         dockerImage = dockerImages["sambamba"]
  79         }
  80
  81         call fgifm2.FilterSamReads as FilterSam {
  82                 input:
  83                         inputBam = markdup.outputBam,
  84                         inputBamIndex = markdup.outputBamIndex,
  85                         outputBamPath = sampleDir + "/" + sample.id + ".fM.bam",
  86                         minMatchLen = minBWAmatchLen
  87         }
  88         call fgifm2.callSNP as fm2callSNP {
  89                 input:
  90                         inputBam = markdup.outputBam,
  91                         inputBamIndex = markdup.outputBamIndex,
  92                         GatkIndex = GatkIndex,
  93                         outputPath = sampleDir + "/SNP/",
  94                         helperPl = "bin/fsnp.pl"
  95         }
  96         call fgifm2.callSTR as fm2callSTR {
  97                 input:
  98                         inputBam = FilterSam.outputBam,
  99                         inputBamIndex = FilterSam.outputBamIndex,
 100                         outputPath = sampleDir + "/STR/",
 101                         helperBED = "bin/LN-mid.bed",
 102                         helperPl = "bin/fstr.pl"
 103         }
 104
 105         output {
 106                 File markdupBam = markdup.outputBam
 107                 File markdupBamIndex = markdup.outputBamIndex
 108                 File filteredBam = FilterSam.outputBam
 109                 File filteredBamIndex = FilterSam.outputBamIndex
 110                 File outSNP0txt = fm2callSNP.outSNP0txt
 111                 File outSTR0txt = fm2callSTR.outSTR0txt
 112                 File outSNP1txt = fm2callSNP.outSNP1txt
 113                 File outSNPtxt = fm2callSNP.outSNPtxt
 114                 File outSTRtxt = fm2callSTR.outSTRtxt
 115                 Array[File] reports = flatten(qualityControl.reports)
 116                 File outbcfFile = fm2callSNP.outbcfFile
 117                 File outsnpFile = fm2callSNP.outsnpFile
 118                 File outsnpIndexFile = fm2callSNP.outsnpIndexFile
 119                 File outsnp0File = fm2callSNP.outsnp0File
 120                 File outsnp0IndexFile = fm2callSNP.outsnp0IndexFile
 121         }
 122
 123         parameter_meta {
 124                 # inputs
 125                 sample: {description: "The sample information: sample id, readgroups, etc.", category: "required"}
 126                 sampleDir: {description: "The directory the output should be written to.", category: "required"}
 127                 platform: {description: "The platform used for sequencing.", category: "advanced"}
 128                 useBwaKit: {description: "Whether or not BWA kit should be used. If false BWA mem will be used.", category: "advanced"}
 129                 bwaIndex: {description: "The BWA index files. These or the bwaMem2Index should be provided.", category: "common"}
 130                 adapterForward: {description: "The adapter to be removed from the reads first or single end reads.", category: "common"}
 131                 adapterReverse: {description: "The adapter to be removed from the reads second end reads.", category: "common"}
 132                 bwaThreads: {description: "The amount of threads for the alignment process.", category: "advanced"}
 133                 dockerImages: {description: "The docker images used.", category: "required"}
 134
 135                 # outputs
 136                 markdupBam: {description: ""}
 137                 markdupBamIndex: {description: ""}
 138                 reports: {description: ""}
 139         }
 140 }
 141