Add container source and version to main workflow***

***Update docker image reference in extract_info task
anand-imcm · Mar 27, 2024 · bb794d7 · bb794d7
1 parent c1bc2af
commit bb794d7
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/workflows/main.wdl b/workflows/main.wdl
@@ -4,6 +4,9 @@ import "./tasks/extract_info.wdl" as info
 
 workflow main {
 
+    String pipeline_version = "1.0.0"
+    String container_src = "ghcr.io/IMCM-OX/get-variant-info:~{pipeline_version}"
+
     input {
         File query_variants
         File? query_samples
@@ -21,7 +24,7 @@ workflow main {
     }
 
     call info.extract {
-        input: query_variants = query_variants, query_samples = query_samples, imputed_vcf = imputed_vcf, prefix = prefix, extract_item = extract_item
+        input: query_variants = query_variants, query_samples = query_samples, imputed_vcf = imputed_vcf, prefix = prefix, extract_item = extract_item, docker = container_src
     }
 
     output {

diff --git a/workflows/tasks/extract_info.wdl b/workflows/tasks/extract_info.wdl
@@ -8,6 +8,7 @@ task extract {
         Array [File] imputed_vcf
         String prefix
         String extract_item
+        String docker
     }
 
     Int disk_size_gb = ceil(size(imputed_vcf, "GiB")) + 5
@@ -54,7 +55,7 @@ task extract {
     }
 
     runtime {
-        docker: "docker.io/library/extract"
+        docker: "~{docker}"
         memory: "32G"
         disks: "local-disk ~{disk_size_gb} HDD"
     }