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1 <macros>
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2 <macro name="main">
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3 <description>Strelka</description>
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4 <requirements>
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5 <requirement type="set_environment">SCRIPT_PATH_STRELKA</requirement>
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6 <requirement type="package" version="0.1.18">samtools</requirement>
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7 <requirement type="package" version="0.1.11">vcftools</requirement>
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8 </requirements>
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9 <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam
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10 #silent sys.stderr.write("!!!! Cheetah Template Variables !!!!\n")
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11 #for k,v in $searchList[2].items()
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12 #silent sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))
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13 #end for
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14 #silent sys.stderr.write("!!!! end-of-list !!!!\n")
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15 #import string
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16
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17 --scriptPath \$SCRIPT_PATH_STRELKA
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18 #if $genomeSource.refGenomeSource == "history":
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19 --refFile "${genomeSource.ownFile}"
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20 #else:
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21 --refFile "${genomeSource.index.fields.path}"
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22 #end if
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23
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24 #if $configuration.configuration_switch == 'Default for Bwa':
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25 --configFile strelka_config_bwa_default.ini
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26 #else if $configuration.configuration_switch == 'Default for Isaac':
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27 --configFile strelka_config_isaac_default.ini
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28 #else if $configuration.configuration_switch == 'Default for Eland':
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29 --configFile strelka_config_eland_default.ini
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30 #else if $configuration.configuration_switch == 'Path':
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31 --configFile $configuration.configFile
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32 #else:
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33 --configFile Custom
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34 --depthFilterMultiple $configuration.depthFilterMultiple
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35 --snvMaxFilteredBasecallFrac $configuration.snvMaxFilteredBasecallFrac
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36 --snvMaxSpanningDeletionFrac $configuration.snvMaxSpanningDeletionFrac
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37 --indelMaxRefRepeat $configuration.indelMaxRefRepeat
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38 --indelMaxWindowFilteredBasecallFrac $configuration.indelMaxWindowFilteredBasecallFrac
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39 --indelMaxIntHpolLength $configuration.indelMaxIntHpolLength
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40 --ssnvPrior $configuration.ssnvPrior
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41 --sindelPrior $configuration.sindelPrior
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42 --ssnvNoise $configuration.ssnvNoise
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43 --sindelNoise $configuration.sindelNoise
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44 --ssnvNoiseStrandBiasFrac $configuration.ssnvNoiseStrandBiasFrac
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45 --minTier1Mapq $configuration.minTier1Mapq
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46 --minTier2Mapq $configuration.minTier2Mapq
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47 --ssnvQuality_LowerBound $configuration.ssnvQuality_LowerBound
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48 --sindelQuality_LowerBound $configuration.sindelQuality_LowerBound
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49 --isWriteRealignedBam $configuration.isWriteRealignedBam
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50 --binSize $configuration.binSize
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51 --isSkipDepthFilters $configuration.isSkipDepthFilters
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52 --maxInputDepth $configuration.maxInputDepth
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53 #if $configuration.extra_arguments.extra_arguments_switch == 'Yes':
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54 --extraStrelkaArguments yes
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55 #if $configuration.extra_arguments.a:
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56 -a
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57 #end if
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58 #if $configuration.extra_arguments.b:
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59 -b $configuration.extra_arguments.barg
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60 #end if
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61 #if $configuration.extra_arguments.c:
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62 -c $configuration.extra_arguments.carg
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63 #end if
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64 #if $configuration.extra_arguments.d:
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65 -d $configuration.extra_arguments.darg
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66 #end if
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67 #if $configuration.extra_arguments.e:
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68 -e $configuration.extra_arguments.earg
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69 #end if
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70 #end if
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71 #end if
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72
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73 </command>
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74 </macro>
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75 </macros>
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76
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