regular wdl looks good

broadinstitute · Mar 18, 2019 · 1da95f5 · 1da95f5
1 parent 33f34b9
commit 1da95f5
Showing 1 changed file with 5 additions and 9 deletions.
diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl
@@ -366,8 +366,6 @@ workflow Mutect2 {
                 gatk_docker = gatk_docker,
                 tumor_pileups = MergeTumorPileups.merged_table,
                 normal_pileups = MergeNormalPileups.merged_table,
-                variants_for_contamination = variants_for_contamination,
-                variants_for_contamination_index = variants_for_contamination_index,
                 disk_space = tumor_bam_size + normal_bam_size + ceil(size(variants_for_contamination, "GB") * small_input_to_output_multiplier) + disk_pad
         }
     }
@@ -638,7 +636,7 @@ task M2 {
             gatk --java-options "-Xmx${command_mem}m" GetPileupSummaries -R ${ref_fasta} -I ${tumor_bam} ${"--interval-set-rule INTERSECTION -L " + intervals} \
                 -V ${variants_for_contamination} -L ${variants_for_contamination} -O tumor-pileups.table
 
-            if [[ ! -z ${normal_bam} ]]; then
+            if [[ ! -z "${normal_bam}" ]]; then
                 gatk --java-options "-Xmx${command_mem}m" GetPileupSummaries -R ${ref_fasta} -I ${normal_bam} ${"--interval-set-rule INTERSECTION -L " + intervals} \
                     -V ${variants_for_contamination} -L ${variants_for_contamination} -O normal-pileups.table
             fi
@@ -948,13 +946,13 @@ task LearnReadOrientationModel {
         export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk_override}
 
         if [[ "${alt_hist_length}" > 0 ]]; then
-            ah_flag="-ah"
+            ah_flag="--alt-hist"
         fi
 
         gatk --java-options "-Xmx${command_mem}m" LearnReadOrientationModel \
-        -at ${sep=" -at " alt_tables} \
-        -rh ${sep=" -rh " ref_histograms} \
-        $ah_flag ${sep=" -ah " alt_histograms} \
+        --alt-table ${sep=" --alt-table " alt_tables} \
+        --ref-hist ${sep=" --ref-hist " ref_histograms} \
+        $ah_flag ${sep=" --alt-hist " alt_histograms} \
         -O "artifact-prior-table.tsv"
     }
 
@@ -981,8 +979,6 @@ task CalculateContamination {
     File ref_dict
     File tumor_pileups
     File? normal_pileups
-    File? variants_for_contamination
-    File? variants_for_contamination_index
 
     File? gatk_override