Add n_files argument to the WDL

UW-GAC · Sep 24, 2024 · 615a0dd · 615a0dd
1 parent e95323f
commit 615a0dd
Showing 1 changed file with 8 additions and 4 deletions.
diff --git a/fetch_dbgap_files.wdl b/fetch_dbgap_files.wdl
@@ -3,16 +3,18 @@ version 1.0
 workflow fetch_dbgap_files {
     input {
         File cart_file
-        File manifest_file
         File ngc_file
         String output_directory
+        File? manifest_file
+        Int? n_files
         Int? disk_gb
     }
 
     call fetch_files {
         input:
             cart_file=cart_file,
             manifest_file=manifest_file,
+            n_files=n_files,
             ngc_file=ngc_file,
             output_directory=output_directory,
             disk_gb=disk_gb
@@ -29,24 +31,26 @@ workflow fetch_dbgap_files {
 task fetch_files {
     input {
         File cart_file
-        File manifest_file
         File ngc_file
         String output_directory
         Int disk_gb = 50
+        File? manifest_file
+        Int? n_files
     }
     command {
         python3 /usr/local/fetch-dbgap-files/fetch.py \
             --prefetch /opt/sratoolkit.3.0.10-ubuntu64/bin/prefetch \
             --ngc ~{ngc_file} \
             --cart ~{cart_file} \
-            --manifest ~{manifest_file} \
+            ~{"--manifest " + manifest_file} \
+            ~{"--n-files " + n_files} \
             --outdir tmp_download \
             --untar
         gsutil -m cp -r tmp_download/* ~{output_directory}
     }
     runtime {
         # Pull from DockerHub
-        docker: "uwgac/fetch-dbgap-files:0.1.0"
+        docker: "uwgac/fetch-dbgap-files:0.2.0"
         disks: "local-disk ${disk_gb} SSD"
     }
 }