fix sage...

sage.wdl

@@ -20,7 +20,7 @@ version 1.0
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-task SageHotspot {
+task Sage {
     input {
         String tumorName
         File tumorBam
@@ -31,17 +31,11 @@ task SageHotspot {
         File referenceFasta
         File referenceFastaDict
         File referenceFastaFai
-<<<<<<< HEAD
         File hotspots
         File panelBed
         File highConfidenceBed
         Boolean hg38 = false
-        String outputPath
-=======
-        File knownHotspots
-        File codingRegsions
         String outputPath = "./sage_hotspot.vcf.gz"
->>>>>>> 2b8e422685de9ea6f63831d8780231a058c1b0cb
 
         Int threads = 2
         String javaXmx = "32G"
@@ -75,12 +69,8 @@ task SageHotspot {
     }
 
     runtime {
-<<<<<<< HEAD
         time_minutes: timeMinutes # !UnknownRuntimeKey
         cpu: threads
-=======
-        time_minutes: timeMinutes
->>>>>>> 2b8e422685de9ea6f63831d8780231a058c1b0cb
         docker: dockerImage
         memory: memory
     }
@@ -108,80 +98,3 @@ task SageHotspot {
                       category: "advanced"}
     }
 }
-
-task Sage {
-    input {
-        String tumorName
-        File tumorBam
-        String? normalName
-        File? normalBam
-        File referenceFasta
-        File referenceFastaFai
-        File referenceFastaDict
-        File hotspots
-        File panelBed
-        File highConfidenceBed
-        String assembly = "hg38"
-        String outputPath = "./sage.vcf.gz"
-
-        Int timeMinutes = 60 #FIXME I've no idea how long this takes...
-        String javaXmx = "32G"
-        String memory = "33G"
-        Int threads = 2
-        String dockerImage = "quay.io/biocontainers/hmftools-sage:2.2--0"
-    }
-
-    command {
-        java -Xmx~{javaXmx} \
-        -cp /usr/local/share/hmftools-sage-2.2-0/sage.jar \
-        com.hartwig.hmftools.sage.SageApplication \
-        -tumor ~{tumorName} \
-        -tumor_bam ~{tumorBam} \
-        ~{"-reference " + normalName} \
-        ~{"-reference_bam " + normalBam} \
-        -ref_genome ~{referenceFasta} \
-        -hotspots ~{hotspots} \
-        -panel_bed ~{panelBed} \
-        -high_confidence_bed ~{highConfidenceBed} \
-        -assembly ~{assembly} \
-        -threads ~{threads} \
-        -out ~{outputPath}
-    }
-
-    output {
-        File outputVcf = outputPath
-    }
-
-    runtime {
-        time_minutes: timeMinutes
-        cpu: threads
-        docker: dockerImage
-        memory: memory
-    }
-
-    parameter_meta {
-        tumorName: {description: "The name of the tumor sample.", category: "required"}
-        tumorBam: {description: "The BAM file for the tumor sample.", category: "required"}
-        tumorBai: {description: "The index of the BAM file for the tumor sample.", category: "required"}
-        normalName: {description: "The name of the normal/reference sample.", category: "common"}
-        normalBam: {description: "The BAM file for the normal sample.", category: "common"}
-        normalBai: {description: "The index of the BAM file for the normal sample.", category: "common"}
-        referenceFasta: {description: "The reference fasta file.", category: "required"}
-        referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
-                             category: "required"}
-        referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
-        hotspots: {description: "A VCF file containg hotspot variant sites.", category: "required"}
-        panelBed: {description: "A bed file containing a panel of genes of intrest.", category: "required"}
-        highConfidenceBed: {description: "A bed file containing high confidence regions.", category: "required"}
-        assembly: {description: "The genome assembly used, either \"hg19\" or \"hg38\".", category: "common"}
-        outputPath: {description: "The path to write the output VCF to.", category: "common"}
-
-        threads: {description: "The number of threads to be used.", category: "advanced"}
-        memory: {description: "The amount of memory this job will use.", category: "advanced"}
-        javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
-                  category: "advanced"}
-        timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
-        dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
-                      category: "advanced"}
-    }
-}
\ No newline at end of file