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Dockerize GATK. Scattering now works with containers. Tabix another docker image.

Merged Dockerize GATK. Scattering now works with containers. Tabix another docker image.
BIOWDL-199 into develop
Merged Ruben Vorderman requested to merge BIOWDL-199 into develop

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gatk.wdl
15 13
16 14 Int memory = 4
17 15 Float memoryMultiplier = 3.0
16 String dockerTag = "4.1.0.0--0"
18 17 }
19 18
20 String toolCommand = if defined(gatkJar)
21 then "java -Xmx" + memory + "G -jar " + gatkJar
22 else "gatk --java-options -Xmx" + memory + "G"
23
24 19 command {
25 20 set -e -o pipefail
26 ~{preCommand}
27 ~{toolCommand} \
28 ApplyBQSR \
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 68ff64af
    • biopet/biopet.wdl
    236 243 Reference reference
    237 String outputDirPath
    238 File? toolJar
    239 244 Int? scatterSize
    240 245 File? regions
    241 246 Boolean notSplitContigs = false
    242
    243 247 Int memory = 4
    244 248 Float memoryMultiplier = 3.0
    249 String dockerTag = "0.2--0"
    245 250 }
    246
    247 String toolCommand = if defined(toolJar)
    248 then "java -Xmx" + memory + "G -jar " +toolJar
    249 else "biopet-scatterregions -Xmx" + memory + "G"
    251 String outputDirPath = "scatters"
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 68ff64af
    • gatk.wdl
    177 161 }
    178 162 }
    179 163
    180 164 task GenotypeGVCFs {
    181 165 input {
    182 String? preCommand
    183 166 Array[File]+ gvcfFiles
    184 167 Array[File]+ gvcfFilesIndex
    185 168 Array[File]+ intervals
    186 169
    187 170 String outputPath
    188 171
    189 String? gatkJar
    190
    191 172 Reference reference
    192 173
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 68ff64af
    • biopet/biopet.wdl
    236 243 Reference reference
    237 String outputDirPath
    238 File? toolJar
    239 244 Int? scatterSize
    240 245 File? regions
    241 246 Boolean notSplitContigs = false
    242
    243 247 Int memory = 4
    244 248 Float memoryMultiplier = 3.0
    249 String dockerTag = "0.2--0"
    245 250 }
    246
    247 String toolCommand = if defined(toolJar)
    248 then "java -Xmx" + memory + "G -jar " +toolJar
    249 else "biopet-scatterregions -Xmx" + memory + "G"
    251 String outputDirPath = "scatters"
    • Ruben Vorderman
      Ruben Vorderman @rhpvorderman ·
      Author Owner

      It was a lot of hassle getting stuff to work correctly with the file localization. But I will return this to normal and see if I can get that working again.

  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 68ff64af
    • gatk.wdl
    177 161 }
    178 162 }
    179 163
    180 164 task GenotypeGVCFs {
    181 165 input {
    182 String? preCommand
    183 166 Array[File]+ gvcfFiles
    184 167 Array[File]+ gvcfFilesIndex
    185 168 Array[File]+ intervals
    186 169
    187 170 String outputPath
    188 171
    189 String? gatkJar
    190
    191 172 Reference reference
    192 173
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 68ff64af
    • biopet/biopet.wdl
    236 243 Reference reference
    237 String outputDirPath
    238 File? toolJar
    239 244 Int? scatterSize
    240 245 File? regions
    241 246 Boolean notSplitContigs = false
    242
    243 247 Int memory = 4
    244 248 Float memoryMultiplier = 3.0
    249 String dockerTag = "0.2--0"
    245 250 }
    246
    247 String toolCommand = if defined(toolJar)
    248 then "java -Xmx" + memory + "G -jar " +toolJar
    249 else "biopet-scatterregions -Xmx" + memory + "G"
    251 String outputDirPath = "scatters"
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 68ff64af
    • biopet/biopet.wdl
    236 243 Reference reference
    237 String outputDirPath
    238 File? toolJar
    239 244 Int? scatterSize
    240 245 File? regions
    241 246 Boolean notSplitContigs = false
    242
    243 247 Int memory = 4
    244 248 Float memoryMultiplier = 3.0
    249 String dockerTag = "0.2--0"
    245 250 }
    246
    247 String toolCommand = if defined(toolJar)
    248 then "java -Xmx" + memory + "G -jar " +toolJar
    249 else "biopet-scatterregions -Xmx" + memory + "G"
    251 String outputDirPath = "scatters"
    • Ruben Vorderman
      Ruben Vorderman @rhpvorderman ·
      Author Owner

      No this will never work. Glob works by linking. And linking between paths inside the container and outside will not work. So no links will appear and the glob will return an empty list. Therefore this can never be changed by the user.

  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 68ff64af
    • biopet/biopet.wdl
    236 243 Reference reference
    237 String outputDirPath
    238 File? toolJar
    239 244 Int? scatterSize
    240 245 File? regions
    241 246 Boolean notSplitContigs = false
    242
    243 247 Int memory = 4
    244 248 Float memoryMultiplier = 3.0
    249 String dockerTag = "0.2--0"
    245 250 }
    246
    247 String toolCommand = if defined(toolJar)
    248 then "java -Xmx" + memory + "G -jar " +toolJar
    249 else "biopet-scatterregions -Xmx" + memory + "G"
    251 String outputDirPath = "scatters"
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 68ff64af
    • biopet/biopet.wdl
    236 243 Reference reference
    237 String outputDirPath
    238 File? toolJar
    239 244 Int? scatterSize
    240 245 File? regions
    241 246 Boolean notSplitContigs = false
    242
    243 247 Int memory = 4
    244 248 Float memoryMultiplier = 3.0
    249 String dockerTag = "0.2--0"
    245 250 }
    246
    247 String toolCommand = if defined(toolJar)
    248 then "java -Xmx" + memory + "G -jar " +toolJar
    249 else "biopet-scatterregions -Xmx" + memory + "G"
    251 String outputDirPath = "scatters"
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