minor mashtree improvements (#142)

* expose docker optional string input for mashtree * added string output "docker" to mashtree task and workflow
theiagen · Aug 7, 2023 · 83f7e39 · 83f7e39
1 parent 5a68417
commit 83f7e39
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diff --git a/tasks/phylogenetic_inference/task_mashtree.wdl b/tasks/phylogenetic_inference/task_mashtree.wdl
@@ -13,6 +13,7 @@ task mashtree_fasta {
     Int cpu = 16
     Int memory = 64
     Int disk_size = 100
+    String docker = "us-docker.pkg.dev/general-theiagen/staphb/mashtree:1.2.0"
   }
   command <<<
     # date and version control
@@ -39,11 +40,12 @@ task mashtree_fasta {
   output {
     String date = read_string("DATE")
     String version = read_string("VERSION")
+    String mashtree_docker = docker
     File mashtree_matrix = "~{cluster_name}.tsv"
     File mashtree_tree = "~{cluster_name}.nwk"
   }
   runtime {
-    docker: "us-docker.pkg.dev/general-theiagen/staphb/mashtree:1.2.0"
+    docker: docker
     memory: "~{memory} GB"
     cpu: cpu
     disks: "local-disk " + disk_size + " SSD"

diff --git a/workflows/phylogenetics/wf_mashtree_fasta.wdl b/workflows/phylogenetics/wf_mashtree_fasta.wdl
@@ -48,6 +48,7 @@ workflow mashtree_fasta {
     File mashtree_matrix = reorder_matrix.ordered_matrix
     File mashtree_tree = reorder_matrix.tree
     String mashtree_version = mashtree_task.version
+    String mashtree_docker = mashtree_task.mashtree_docker
     # Data Summary Out
     File? mashtree_summarized_data = summarize_data.summarized_data
     File? mashtree_filtered_metadata = summarize_data.filtered_metadata