update task name from transfer to list, decrease memory and cpu, make…

… task premptible

tasks/utilities/file_handling/task_transfer_pod5_files.wdl → tasks/utilities/file_handling/task_list_pod5_files.wdl

@@ -1,11 +1,11 @@
 version 1.0
 
-task transfer_pod5_files {
+task list_pod5_files {
   input {
     String pod5_bucket_path             # GCS bucket path containing `.pod5` files (e.g., "gs://your-terra-bucket/pod5_uploads/")
     Int disk_size = 100
-    Int memory = 32
-    Int cpu = 8
+    Int memory = 4
+    Int cpu = 1
     String docker =  "us-docker.pkg.dev/general-theiagen/cloudsdktool/google-cloud-cli:427.0.0-alpine"
   }
   command <<<
@@ -28,7 +28,7 @@ task transfer_pod5_files {
     cpu: cpu
     memory: "~{memory} GB"
     disks: "local-disk ~{disk_size} SSD"
-    preemptible: 0
+    preemptible: 1
     maxRetries: 1
   }
 }

workflows/utilities/wf_dorado_basecalling.wdl

@@ -6,7 +6,7 @@ import "../../tasks/basecalling/task_dorado_demux.wdl" as dorado_demux_task
 import "../../tasks/utilities/file_handling/task_transfer_files.wdl" as transfer_fastq_files
 import "../../tasks/utilities/data_import/task_create_terra_table.wdl" as terra_fastq_table
 import "../../tasks/task_versioning.wdl" as versioning_task
-import "../../tasks/utilities/file_handling/task_transfer_pod5_files.wdl" as transfer_pod5_files_task         
+import "../../tasks/utilities/file_handling/task_list_pod5_files.wdl" as list_pod5_files_task         
 
 workflow dorado_basecalling_workflow {
   meta {
@@ -28,11 +28,11 @@ workflow dorado_basecalling_workflow {
   call versioning_task.version_capture {
     input:
   }
-  call transfer_pod5_files_task.transfer_pod5_files as transfer_pod5 {
+  call list_pod5_files_task.list_pod5_files as list_pod5 {
     input:
       pod5_bucket_path = pod5_bucket_path
   }
-  scatter (pod5_path in transfer_pod5.pod5_file_paths) {
+  scatter (pod5_path in list_pod5.pod5_file_paths) {
     call basecall_task.basecall as dorado_basecall {
       input:
         input_file = pod5_path,