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minor mashtree improvements #142

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merged 2 commits into from
Aug 7, 2023
Merged

minor mashtree improvements #142

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3f911bf
expose docker optional string input for mashtree
kapsakcj Aug 3, 2023
194d4c2
added string output "docker" to mashtree task and workflow
kapsakcj Aug 3, 2023
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4 changes: 3 additions & 1 deletion tasks/phylogenetic_inference/task_mashtree.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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"
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1 change: 1 addition & 0 deletions workflows/phylogenetics/wf_mashtree_fasta.wdl
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Expand Up @@ -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
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