add a task to the bulk download that renames the output file (#341)

chanzuckerberg · Mar 29, 2024 · 5bfe461 · 5bfe461
1 parent 386bf7b
commit 5bfe461
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Showing 2 changed files with 42 additions and 15 deletions.
diff --git a/workflows/bulk-download/manifest.yml b/workflows/bulk-download/manifest.yml
@@ -2,15 +2,10 @@ workflow_name: bulk-download
 specification_language: WDL
 description: Generate bulk downloads for the CZID web application
 entity_inputs:
-  files:
-    name: Files
-    description: Files to zip or concatenate together 
-    entity_type: file
-    multivalue: True
-  samples:
-    name: Samples
-    description: Optionally associate this bulk download with some samples
-    entity_type: sample
+  consensus_genomes:
+    name: Consensus Genomes
+    description: Consensus genomes to bulk download
+    entity_type: consensus_genome
     multivalue: True
     required: False
 raw_inputs:
@@ -29,10 +24,11 @@ raw_inputs:
       - consensus_genome
       - consensus_genome_intermediate_output_files
 input_loaders:
-  - name: files
+  - name: bulk_download
     version: ">=0.0.1"
     inputs:
-      files: ~
+      consensus_genomes: ~
+      bulk_download_type: ~
     outputs:
       files: ~
   - name: passthrough

diff --git a/workflows/bulk-download/run.wdl b/workflows/bulk-download/run.wdl
@@ -1,24 +1,38 @@
 version 1.1
 
+struct BulkDownloads { 
+    File file_path
+    String output_name
+}
+
 workflow bulk_download {
     input {
         String action
-        Array[File] files
+        Array[BulkDownloads] files
         String docker_image_id = "czid-bulk-download"
     }
 
+    scatter (file in files) {
+        call rename {
+            input: 
+                input_file = file.file_path,
+                output_name = file.output_name,
+                docker_image_id = docker_image_id
+        }
+    }
+
     if (action == "concatenate") {
         call concatenate { 
             input:
-                files = files,
+                files = rename.file,
                 docker_image_id = docker_image_id
         }
     }
 
     if (action == "zip") {
         call zip { 
             input:
-                files = files,
+                files = rename.file,
                 docker_image_id = docker_image_id
         }
     }
@@ -28,6 +42,24 @@ workflow bulk_download {
     }
 }
 
+task rename { 
+    input {
+        String docker_image_id
+        File input_file
+        String output_name
+    }
+    command <<<
+        set -euxo pipefail
+        cp "~{input_file}" "~{output_name}"
+    >>>
+    output {
+        File file = "~{output_name}"
+    }
+    runtime { 
+        docker: docker_image_id
+    }
+}
+
 task concatenate {
     input {
         String docker_image_id
@@ -52,7 +84,6 @@ task zip {
     }
     command <<<
         set -euxo pipefail
-
         # Don't store full path of original files in the .zip file
         zip --junk-paths result.zip ~{sep=" " files}
     >>>