change runtime attrs to args in MT pipeline (#8413)

broadinstitute · Jul 11, 2023 · e0090de · e0090de
1 parent 9216207
commit e0090de
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Showing 3 changed files with 16 additions and 12 deletions.
diff --git a/scripts/mitochondria_m2_wdl/AlignAndCall.wdl b/scripts/mitochondria_m2_wdl/AlignAndCall.wdl
@@ -308,12 +308,13 @@ task CollectWgsMetrics {
     Int? read_length
     Int? coverage_cap
 
+    # runtime
     Int? preemptible_tries
+    Int disk_size = ceil(size(input_bam, "GB") + size(ref_fasta, "GB") + size(ref_fasta_index, "GB")) + 20
+    Int mem = 3
   }
 
   Int read_length_for_optimization = select_first([read_length, 151])
-  Float ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB")
-  Int disk_size = ceil(size(input_bam, "GB") + ref_size) + 20
 
   meta {
     description: "Collect coverage metrics"
@@ -345,7 +346,7 @@ task CollectWgsMetrics {
   >>>
   runtime {
     preemptible: select_first([preemptible_tries, 5])
-    memory: "3 GB"
+    memory: mem + " GB"
     disks: "local-disk " + disk_size + " HDD"
     docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
   }
@@ -426,16 +427,16 @@ task M2 {
     Boolean? make_bamout
     Boolean compress
     File? gatk_override
+   
     # runtime
     String? gatk_docker_override
     Int? mem
     Int? preemptible_tries
+    Int disk_size = ceil(size(input_bam, "GB") + size(ref_fasta, "GB") + size(ref_fai, "GB")) + 20
   }
 
   String output_vcf = "raw" + if compress then ".vcf.gz" else ".vcf"
   String output_vcf_index = output_vcf + if compress then ".tbi" else ".idx"
-  Float ref_size = size(ref_fasta, "GB") + size(ref_fai, "GB")
-  Int disk_size = ceil(size(input_bam, "GB") + ref_size) + 20
 
   # 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 3500

diff --git a/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl b/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl
@@ -70,13 +70,14 @@ task AlignAndMarkDuplicates {
 
     String? read_name_regex
 
+    # runtime
     Int? preemptible_tries
+    Int disk_size = ceil(size(input_bam, "GB") * 4 + size(ref_fasta, "GB") + size(ref_fasta_index, "GB") + size(ref_amb, "GB") + size(ref_ann, "GB") + size(ref_bwt, "GB") + size(ref_pac, "GB") + size(ref_sa, "GB")) + 20
+    Int mem = 6
   }
 
   String basename = basename(input_bam, ".bam")
   String metrics_filename = basename + ".metrics"
-  Float ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB") + size(ref_amb, "GB") + size(ref_ann, "GB") + size(ref_bwt, "GB") + size(ref_pac, "GB") + size(ref_sa, "GB")
-  Int disk_size = ceil(size(input_bam, "GB") * 4 + ref_size) + 20
 
   meta {
     description: "Aligns with BWA and MergeBamAlignment, then Marks Duplicates. Outputs a coordinate sorted bam."
@@ -149,7 +150,7 @@ task AlignAndMarkDuplicates {
   >>>
   runtime {
     preemptible: select_first([preemptible_tries, 5])
-    memory: "6 GB"
+    memory: mem + " GB"
     cpu: "2"
     disks: "local-disk " + disk_size + " HDD"
     docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"

diff --git a/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl b/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
@@ -201,6 +201,7 @@ task SubsetBamToChrM {
 
     # runtime
     Int? preemptible_tries
+    Int mem = 3
   }
   Float ref_size = if defined(ref_fasta) then size(ref_fasta, "GB") + size(ref_fasta_index, "GB") + size(ref_dict, "GB") else 0
   Int disk_size = ceil(size(input_bam, "GB") + ref_size) + 20
@@ -232,7 +233,7 @@ task SubsetBamToChrM {
       -O ~{basename}.bam
   >>>
   runtime {
-    memory: "3 GB"
+    memory: mem + " GB"
     disks: "local-disk " + disk_size + " HDD"
     docker: select_first([gatk_docker_override, "us.gcr.io/broad-gatk/gatk:4.1.7.0"])
     preemptible: select_first([preemptible_tries, 5])
@@ -247,12 +248,12 @@ task RevertSam {
   input {
     File input_bam
     String basename = basename(input_bam, ".bam")
-    Int machine_mem = 2000
 
     # runtime
     Int? preemptible_tries
+    Int machine_mem = 2000
+    Int disk_size = ceil(size(input_bam, "GB") * 2.5) + 20
   }
-  Int disk_size = ceil(size(input_bam, "GB") * 2.5) + 20
   Int java_mem = machine_mem - 1000
 
   meta {
@@ -300,9 +301,10 @@ task CoverageAtEveryBase {
     File shifted_ref_fasta_index
     File shifted_ref_dict
 
+    # runtime
     Int? preemptible_tries
+    Int disk_size = ceil(size(input_bam_regular_ref, "GB") + size(input_bam_shifted_ref, "GB") + size(ref_fasta, "GB") * 2) + 20
   }
-  Int disk_size = ceil(size(input_bam_regular_ref, "GB") + size(input_bam_shifted_ref, "GB") + size(ref_fasta, "GB") * 2) + 20
 
   meta {
     description: "Remove this hack once there's a GVCF solution."