Standardized use of mem parameters in CNV WDLs. (#4193)

broadinstitute · Jan 22, 2018 · 32f25b9 · 32f25b9
1 parent a4bf560
commit 32f25b9
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Showing 6 changed files with 93 additions and 86 deletions.
diff --git a/scripts/cnv_wdl/cnv_common_tasks.wdl b/scripts/cnv_wdl/cnv_common_tasks.wdl
@@ -8,11 +8,14 @@ task PreprocessIntervals {
     File? gatk4_jar_override
 
     # Runtime parameters
-    Int? mem
+    Int? mem_gb
     String gatk_docker
     Int? preemptible_attempts
     Int? disk_space_gb
 
+    Int machine_mem_mb = select_first([mem_gb, 2]) * 1000
+    Int command_mem_mb = machine_mem_mb - 500
+
     # Determine output filename
     String filename = select_first([intervals, "wgs"])
     String base_filename = basename(filename, ".interval_list")
@@ -21,7 +24,7 @@ task PreprocessIntervals {
         set -e
         export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}
 
-        gatk --java-options "-Xmx${default="2" mem}g" PreprocessIntervals \
+        gatk --java-options "-Xmx${command_mem_mb}m" PreprocessIntervals \
             ${"-L " + intervals} \
             --sequence-dictionary ${ref_fasta_dict} \
             --reference ${ref_fasta} \
@@ -33,7 +36,7 @@ task PreprocessIntervals {
 
     runtime {
         docker: "${gatk_docker}"
-        memory: select_first([mem, 2]) + " GB"
+        memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, 40]) + " HDD"
         preemptible: select_first([preemptible_attempts, 5])
     }
@@ -51,16 +54,19 @@ task AnnotateIntervals {
     File? gatk4_jar_override
 
     # Runtime parameters
-    Int? mem
+    Int? mem_gb
     String gatk_docker
     Int? preemptible_attempts
     Int? disk_space_gb
 
+    Int machine_mem_mb = select_first([mem_gb, 2]) * 1000
+    Int command_mem_mb = machine_mem_mb - 500
+
     command <<<
         set -e
         export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}
 
-        gatk --java-options "-Xmx${default="4" mem}g" AnnotateIntervals \
+        gatk --java-options "-Xmx${command_mem_mb}m" AnnotateIntervals \
             -L ${intervals} \
             --reference ${ref_fasta} \
             --interval-merging-rule OVERLAPPING_ONLY \
@@ -69,7 +75,7 @@ task AnnotateIntervals {
 
     runtime {
         docker: "${gatk_docker}"
-        memory: select_first([mem, 5]) + " GB"
+        memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, ceil(size(ref_fasta, "GB")) + 50]) + " HDD"
         preemptible: select_first([preemptible_attempts, 5])
     }
@@ -87,11 +93,14 @@ task CollectCounts {
     File? gatk4_jar_override
 
     # Runtime parameters
-    Int? mem
+    Int? mem_gb
     String gatk_docker
     Int? preemptible_attempts
     Int? disk_space_gb
 
+    Int machine_mem_mb = select_first([mem_gb, 7]) * 1000
+    Int command_mem_mb = machine_mem_mb - 1000
+
     # Sample name is derived from the bam filename
     String base_filename = basename(bam, ".bam")
     String counts_filename = if !defined(format) then "${base_filename}.counts.hdf5" else "${base_filename}.counts.tsv"
@@ -100,7 +109,7 @@ task CollectCounts {
         set -e
         export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}
 
-        gatk --java-options "-Xmx${default="8" mem}g" CollectFragmentCounts \
+        gatk --java-options "-Xmx${command_mem_mb}m" CollectFragmentCounts \
             --input ${bam} \
             -L ${intervals} \
             --format ${default="HDF5" format} \
@@ -110,7 +119,7 @@ task CollectCounts {
 
     runtime {
         docker: "${gatk_docker}"
-        memory: select_first([mem, 8]) + " GB"
+        memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, ceil(size(bam, "GB")) + 50]) + " HDD"
         preemptible: select_first([preemptible_attempts, 5])
     }
@@ -132,14 +141,13 @@ task CollectAllelicCounts {
     File? gatk4_jar_override
 
     # Runtime parameters
-    Int? mem
+    Int? mem_gb
     String gatk_docker
     Int? preemptible_attempts
     Int? disk_space_gb
 
-    # Mem is in units of GB but our command and memory runtime values are in MB
-    Int machine_mem = if defined(mem) then mem * 1000 else 13000
-    Int command_mem = machine_mem - 1000
+    Int machine_mem_mb = select_first([mem_gb, 13]) * 1000
+    Int command_mem_mb = machine_mem_mb - 1000
 
     # Sample name is derived from the bam filename
     String base_filename = basename(bam, ".bam")
@@ -150,7 +158,7 @@ task CollectAllelicCounts {
         set -e
         export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}
 
-        gatk --java-options "-Xmx${command_mem}m" CollectAllelicCounts \
+        gatk --java-options "-Xmx${command_mem_mb}m" CollectAllelicCounts \
             -L ${common_sites} \
             --input ${bam} \
             --reference ${ref_fasta} \
@@ -160,7 +168,7 @@ task CollectAllelicCounts {
 
     runtime {
         docker: "${gatk_docker}"
-        memory: machine_mem + " MB"
+        memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, ceil(size(bam, "GB")) + 50]) + " HDD"
         preemptible: select_first([preemptible_attempts, 5])
     }
@@ -176,11 +184,13 @@ task ScatterIntervals {
     Int num_intervals_per_scatter
 
     # Runtime parameters
-    Int? mem
+    Int? mem_gb
     String gatk_docker
     Int? preemptible_attempts
     Int? disk_space_gb
 
+    Int machine_mem_mb = select_first([mem_gb, 2]) * 1000
+
     String base_filename = basename(interval_list, ".interval_list")
 
     command <<<
@@ -194,7 +204,7 @@ task ScatterIntervals {
 
     runtime {
         docker: "${gatk_docker}"
-        memory: select_first([mem, 2]) + " GB"
+        memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, 40]) + " HDD"
         preemptible: select_first([preemptible_attempts, 5])
     }

diff --git a/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
@@ -38,8 +38,8 @@ workflow CNVGermlineCaseWorkflow {
     #### optional basic arguments ####
     ##################################
     File? gatk4_jar_override
-    Int? mem_for_determine_germline_contig_ploidy
-    Int? mem_for_germline_cnv_caller
+    Int? mem_gb_for_determine_germline_contig_ploidy
+    Int? mem_gb_for_germline_cnv_caller
     Int? cpu_for_determine_germline_contig_ploidy
     Int? cpu_for_germline_cnv_caller
     Int? preemptible_attempts
@@ -116,7 +116,7 @@ workflow CNVGermlineCaseWorkflow {
             contig_ploidy_model_tar = contig_ploidy_model_tar,
             gatk4_jar_override = gatk4_jar_override,
             gatk_docker = gatk_docker,
-            mem = mem_for_determine_germline_contig_ploidy,
+            mem_gb = mem_for_determine_germline_contig_ploidy,
             cpu = cpu_for_determine_germline_contig_ploidy,
             mapping_error_rate = ploidy_mapping_error_rate,
             sample_psi_scale = ploidy_sample_psi_scale,
@@ -141,7 +141,7 @@ workflow CNVGermlineCaseWorkflow {
                 intervals = ScatterIntervals.scattered_interval_lists[scatter_index],
                 gatk4_jar_override = gatk4_jar_override,
                 gatk_docker = gatk_docker,
-                mem = mem_for_germline_cnv_caller,
+                mem_gb = mem_for_germline_cnv_caller,
                 cpu = cpu_for_germline_cnv_caller,
                 p_alt = gcnv_p_alt,
                 cnv_coherence_length = gcnv_cnv_coherence_length,
@@ -190,7 +190,7 @@ task DetermineGermlineContigPloidyCaseMode {
     File? gatk4_jar_override
 
     # Runtime parameters
-    Int? mem
+    Int? mem_gb
     Int? cpu
     String gatk_docker
     Int? preemptible_attempts
@@ -202,8 +202,8 @@ task DetermineGermlineContigPloidyCaseMode {
 
     # We do not expose Hybrid ADVI parameters -- the default values are decent
 
-    Int machine_mem = if defined(mem) then select_first([mem]) else 8
-    Float command_mem = machine_mem - 0.5
+    Int machine_mem_mb = select_first([mem_gb, 7]) * 1000
+    Int command_mem_mb = machine_mem_mb - 500
 
     # If optional output_dir not specified, use "out"
     String output_dir_ = select_first([output_dir, "out"])
@@ -218,7 +218,7 @@ task DetermineGermlineContigPloidyCaseMode {
         mkdir input-contig-ploidy-model
         tar xzf ${contig_ploidy_model_tar} -C input-contig-ploidy-model
 
-        gatk --java-options "-Xmx${machine_mem}g" DetermineGermlineContigPloidy \
+        gatk --java-options "-Xmx${command_mem_mb}m" DetermineGermlineContigPloidy \
             --input ${sep=" --input " read_count_files} \
             --model input-contig-ploidy-model \
             --output ${output_dir_} \
@@ -232,7 +232,7 @@ task DetermineGermlineContigPloidyCaseMode {
 
     runtime {
         docker: "${gatk_docker}"
-        memory: command_mem + " GB"
+        memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, 150]) + " HDD"
         preemptible: select_first([preemptible_attempts, 2])
         cpu: select_first([cpu, 8])
@@ -254,7 +254,7 @@ task GermlineCNVCallerCaseMode {
     File? gatk4_jar_override
 
     # Runtime parameters
-    Int? mem
+    Int? mem_gb
     Int? cpu
     String gatk_docker
     Int? preemptible_attempts
@@ -293,8 +293,8 @@ task GermlineCNVCallerCaseMode {
     Float? caller_admixing_rate
     Boolean? disable_annealing
 
-    Int machine_mem = if defined(mem) then select_first([mem]) else 8
-    Float command_mem = machine_mem - 0.5
+    Int machine_mem_mb = select_first([mem_gb, 7]) * 1000
+    Int command_mem_mb = machine_mem_mb - 500
 
     # If optional output_dir not specified, use "out"
     String output_dir_ = select_first([output_dir, "out"])
@@ -312,7 +312,7 @@ task GermlineCNVCallerCaseMode {
         mkdir gcnv-model
         tar xzf ${gcnv_model_tar} -C gcnv-model
 
-        gatk --java-options "-Xmx${machine_mem}g"  GermlineCNVCaller \
+        gatk --java-options "-Xmx${command_mem_mb}m"  GermlineCNVCaller \
             --run-mode CASE \
             --input ${sep=" --input " read_count_files} \
             --contig-ploidy-calls contig-ploidy-calls-dir \
@@ -353,7 +353,7 @@ task GermlineCNVCallerCaseMode {
 
     runtime {
         docker: "${gatk_docker}"
-        memory: command_mem + " GB"
+        memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, 150]) + " HDD"
         preemptible: select_first([preemptible_attempts, 2])
         cpu: select_first([cpu, 8])

diff --git a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
@@ -36,8 +36,8 @@ workflow CNVGermlineCohortWorkflow {
     #### optional basic arguments ####
     ##################################
     File? gatk4_jar_override
-    Int? mem_for_determine_germline_contig_ploidy
-    Int? mem_for_germline_cnv_caller
+    Int? mem_gb_for_determine_germline_contig_ploidy
+    Int? mem_gb_for_germline_cnv_caller
     Int? cpu_for_determine_germline_contig_ploidy
     Int? cpu_for_germline_cnv_caller
     Int? preemptible_attempts
@@ -147,7 +147,7 @@ workflow CNVGermlineCohortWorkflow {
             contig_ploidy_priors = contig_ploidy_priors,
             gatk4_jar_override = gatk4_jar_override,
             gatk_docker = gatk_docker,
-            mem = mem_for_determine_germline_contig_ploidy,
+            mem_gb = mem_for_determine_germline_contig_ploidy,
             cpu = cpu_for_determine_germline_contig_ploidy,
             mean_bias_standard_deviation = ploidy_mean_bias_standard_deviation,
             mapping_error_rate = ploidy_mapping_error_rate,
@@ -175,7 +175,7 @@ workflow CNVGermlineCohortWorkflow {
                 annotated_intervals = AnnotateIntervals.annotated_intervals,
                 gatk4_jar_override = gatk4_jar_override,
                 gatk_docker = gatk_docker,
-                mem = mem_for_germline_cnv_caller,
+                mem_gb = mem_for_germline_cnv_caller,
                 cpu = cpu_for_germline_cnv_caller,
                 p_alt = gcnv_p_alt,
                 p_active = gcnv_p_active,
@@ -234,7 +234,7 @@ task DetermineGermlineContigPloidyCohortMode {
     File? gatk4_jar_override
 
     # Runtime parameters
-    Int? mem
+    Int? mem_gb
     Int? cpu
     String gatk_docker
     Int? preemptible_attempts
@@ -248,8 +248,8 @@ task DetermineGermlineContigPloidyCohortMode {
 
     # We do not expose Hybrid ADVI parameters -- the default values are decent
 
-    Int machine_mem = if defined(mem) then select_first([mem]) else 8
-    Float command_mem = machine_mem - 0.5
+    Int machine_mem_mb = select_first([mem_gb, 7]) * 1000
+    Int command_mem_mb = machine_mem_mb - 500
 
     # If optional output_dir not specified, use "out"
     String output_dir_ = select_first([output_dir, "out"])
@@ -261,7 +261,7 @@ task DetermineGermlineContigPloidyCohortMode {
         export MKL_NUM_THREADS=${default=8 cpu}
         export OMP_NUM_THREADS=${default=8 cpu}
 
-        gatk --java-options "-Xmx${machine_mem}g"  DetermineGermlineContigPloidy \
+        gatk --java-options "-Xmx${command_mem_mb}m"  DetermineGermlineContigPloidy \
             --input ${sep=" --input " read_count_files} \
             --contig-ploidy-priors ${contig_ploidy_priors} \
             --output ${output_dir_} \
@@ -278,7 +278,7 @@ task DetermineGermlineContigPloidyCohortMode {
 
     runtime {
         docker: "${gatk_docker}"
-        memory: command_mem + " GB"
+        memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, 150]) + " HDD"
         preemptible: select_first([preemptible_attempts, 2])
         cpu: select_first([cpu, 8])
@@ -301,7 +301,7 @@ task GermlineCNVCallerCohortMode {
     File? gatk4_jar_override
 
     # Runtime parameters
-    Int? mem
+    Int? mem_gb
     Int? cpu
     String gatk_docker
     Int? preemptible_attempts
@@ -349,8 +349,8 @@ task GermlineCNVCallerCohortMode {
     Float? caller_admixing_rate
     Boolean? disable_annealing
 
-    Int machine_mem = if defined(mem) then select_first([mem]) else 8
-    Float command_mem = machine_mem - 0.5
+    Int machine_mem_mb = select_first([mem_gb, 7]) * 1000
+    Int command_mem_mb = machine_mem_mb - 500
 
     # If optional output_dir not specified, use "out"
     String output_dir_ = select_first([output_dir, "out"])
@@ -365,7 +365,7 @@ task GermlineCNVCallerCohortMode {
         mkdir contig-ploidy-calls-dir
         tar xzf ${contig_ploidy_calls_tar} -C contig-ploidy-calls-dir
 
-        gatk --java-options "-Xmx${machine_mem}g"  GermlineCNVCaller \
+        gatk --java-options "-Xmx${command_mem_mb}m"  GermlineCNVCaller \
             --run-mode COHORT \
             -L ${intervals} \
             --input ${sep=" --input " read_count_files} \
@@ -418,7 +418,7 @@ task GermlineCNVCallerCohortMode {
 
     runtime {
         docker: "${gatk_docker}"
-        memory: command_mem + " GB"
+        memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, 150]) + " HDD"
         preemptible: select_first([preemptible_attempts, 2])
         cpu: select_first([cpu, 8])