From 1c8f0caebcd9e77c7d1e4a03c62ecc6f0cf29cd1 Mon Sep 17 00:00:00 2001
From: "Stephanie M. Gogarten" <sdmorris@uw.edu>
Date: Fri, 9 Aug 2024 09:50:11 -0700
Subject: [PATCH] set disk size and memory requirements, use newer docker

---
 plink2_bed2vcf.wdl  |  2 +-
 plink2_pgen2bed.wdl | 18 +++++++++++-------
 plink2_pgen2vcf.wdl | 18 +++++++++++-------
 plink2_vcf2bed.wdl  |  6 +++++-
 plink2_vcf2pgen.wdl |  6 +++++-
 5 files changed, 33 insertions(+), 17 deletions(-)

diff --git a/plink2_bed2vcf.wdl b/plink2_bed2vcf.wdl
index eb85ab0..11e8e13 100644
--- 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
index 63578f4..28a4bff 100644
--- 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
index 27666a5..05f3f2b 100644
--- 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
index f0078fe..0a70cdc 100644
--- 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
index e6035a4..859123b 100644
--- 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"
     }
 }