build-out task

Author: xonq

tasks/utilities/data_handling/task_phylovalidate.wdl

@@ -0,0 +1,47 @@
+version 1.0
+
+task phylovalidate {
+  input {
+    File tree1_path
+    File tree2_path
+
+    Float? rf_max_distance = 0.0
+    Boolean? unrooted = true
+    
+    String docker = "us-docker.pkg.dev/general-theiagen/theiagen/theiavalidate:0.1.0"  # update!!!
+    Int disk_size = 10
+    Int memory = 4
+    Int cpu = 1
+  }
+  meta {
+    # added so that call caching is always turned off
+    volatile: true
+  }
+  command <<<
+    # grab the ete3 version
+    ete3 --version > VERSION
+
+    # run ete3 compare
+    if ~{unrooted}; then
+      ete3 compare -t ~{tree1_path} -r ~{tree2_path} --unrooted --show_mismatches > phylocompare.txt
+    else
+      ete3 compare -t ~{tree1_path} -r ~{tree2_path} --show_mismatches > phylocompare.txt
+    fi
+
+    # extract the RF distance
+    tail -1 phylocompare.txt | cut -f 5 -d '|' | tr -d ' ' > PHYLOCOMPARE_RF_DISTANCE
+  >>>
+  runtime {
+    docker: docker 
+    memory: memory + " GB"
+    cpu: cpu
+    disks:  "local-disk " + disk_size + " HDD"
+    disk: disk_size + " GB"
+    dx_instance_type: "mem1_ssd1_v2_x2"
+  }
+  output {
+    String ete3_version = read_string("VERSION")
+    File summary_report = "phylocompare.txt"
+    Float rf_distance = read_float("PHYLOCOMPARE_RF_DISTANCE")
+  }
+}