set disk size and memory requirements, use newer docker

UW-GAC · Aug 9, 2024 · 1c8f0ca · 1c8f0ca
1 parent 4f85918
commit 1c8f0ca
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Showing 5 changed files with 33 additions and 17 deletions.
diff --git a/plink2_bed2vcf.wdl b/plink2_bed2vcf.wdl
@@ -70,7 +70,7 @@ task bed2vcf {
     }
 
     runtime {
-        docker: "quay.io/biocontainers/plink2:2.00a3.3--hb2a7ceb_0"
+        docker: "quay.io/biocontainers/plink2:2.00a5.10--h4ac6f70_0"
         disks: "local-disk " + disk_size + " SSD"
         memory: mem_gb + " GB"
     }

diff --git a/plink2_pgen2bed.wdl b/plink2_pgen2bed.wdl
@@ -2,9 +2,9 @@ version 1.0
 
 workflow plink2_pgen2bed {
     input {
-		File pgen
-		File pvar
-		File psam
+        File pgen
+        File pvar
+        File psam
         String? out_prefix
     }
 
@@ -30,12 +30,14 @@ workflow plink2_pgen2bed {
 
 task pgen2bed {
     input {
-		File pgen
-		File pvar
-		File psam
+        File pgen
+        File pvar
+        File psam
         String? out_prefix
+        Int mem_gb = 16
     }
 
+    Int disk_size = ceil(3*(size(pgen, "GB") + size(pvar, "GB") + size(psam, "GB"))) + 10
     String out_string = if defined(out_prefix) then out_prefix else basename(pgen, ".pgen")
 
     command {
@@ -60,6 +62,8 @@ task pgen2bed {
     }
 
     runtime {
-        docker: "quay.io/biocontainers/plink2:2.00a3.3--hb2a7ceb_0"
+        docker: "quay.io/biocontainers/plink2:2.00a5.10--h4ac6f70_0"
+        disks: "local-disk " + disk_size + " SSD"
+        memory: mem_gb + " GB"
     }
 }
diff --git a/plink2_pgen2vcf.wdl b/plink2_pgen2vcf.wdl
@@ -2,9 +2,9 @@ version 1.0
 
 workflow plink2_pgen2vcf {
     input {
-		File pgen
-		File pvar
-		File psam
+        File pgen
+        File pvar
+        File psam
         String? out_prefix
     }
 
@@ -28,12 +28,14 @@ workflow plink2_pgen2vcf {
 
 task pgen2vcf {
     input {
-		File pgen
-		File pvar
-		File psam
+        File pgen
+        File pvar
+        File psam
         String? out_prefix
+        Int mem_gb = 16
     }
 
+    Int disk_size = ceil(3*(size(pgen, "GB") + size(pvar, "GB") + size(psam, "GB"))) + 10
     String out_string = if defined(out_prefix) then out_prefix else basename(pgen, ".pgen")
 
     command {
@@ -50,6 +52,8 @@ task pgen2vcf {
     }
 
     runtime {
-        docker: "quay.io/biocontainers/plink2:2.00a3.3--hb2a7ceb_0"
+        docker: "quay.io/biocontainers/plink2:2.00a5.10--h4ac6f70_0"
+        disks: "local-disk " + disk_size + " SSD"
+        memory: mem_gb + " GB"
     }
 }
diff --git a/plink2_vcf2bed.wdl b/plink2_vcf2bed.wdl
@@ -28,8 +28,10 @@ task vcf2bed {
     input {
         File vcf_file
         String? out_prefix
+        Int mem_gb = 16
     }
 
+    Int disk_size = ceil(3*(size(vcf_file, "GB"))) + 10
     String out_string = if defined(out_prefix) then out_prefix else basename(vcf_file, ".vcf.gz")
 
     command {
@@ -54,6 +56,8 @@ task vcf2bed {
     }
 
     runtime {
-        docker: "quay.io/biocontainers/plink2:2.00a3.3--hb2a7ceb_0"
+        docker: "quay.io/biocontainers/plink2:2.00a5.10--h4ac6f70_0"
+        disks: "local-disk " + disk_size + " SSD"
+        memory: mem_gb + " GB"
     }
 }
diff --git a/plink2_vcf2pgen.wdl b/plink2_vcf2pgen.wdl
@@ -28,8 +28,10 @@ task vcf2pgen {
     input {
         File vcf_file
         String? out_prefix
+        Int mem_gb = 16
     }
 
+    Int disk_size = ceil(3*(size(vcf_file, "GB"))) + 10
     String out_string = if defined(out_prefix) then out_prefix else basename(vcf_file, ".vcf.gz")
 
     command {
@@ -54,6 +56,8 @@ task vcf2pgen {
     }
 
     runtime {
-        docker: "quay.io/biocontainers/plink2:2.00a3.3--hb2a7ceb_0"
+        docker: "quay.io/biocontainers/plink2:2.00a5.10--h4ac6f70_0"
+        disks: "local-disk " + disk_size + " SSD"
+        memory: mem_gb + " GB"
     }
 }