Workaround CWL limit by chunking file list

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

1 files changed, 39 insertions, 7 deletions

diff --git a/workflows/pangenome-generate/merge-metadata.cwl b/workflows/pangenome-generate/merge-metadata.cwl
index fcefe32..4d9c808 100644
--- a/workflows/pangenome-generate/merge-metadata.cwl
+++ b/workflows/pangenome-generate/merge-metadata.cwl
@@ -5,16 +5,48 @@ hints:
     dockerPull: commonworkflowlanguage/cwltool_module
 inputs:
   metadata: File[]
-  metadataSchema: File
   subjects: string[]
-  dups: File?
-  originalLabels: File
+  metadataSchema:
+    type: File
+    inputBinding: {position: 2}
+  originalLabels:
+    type: File
+    inputBinding: {position: 3}
+  dups:
+    type: File?
+    inputBinding: {position: 4}
+  script:
+    type: File
+    inputBinding: {position: 1}
+    default: {class: File, location: merge-metadata.py}
 outputs:
   merged: stdout
 stdout: mergedmetadata.ttl
 requirements:
+  InlineJavascriptRequirement: {}
   InitialWorkDirRequirement:
-    listing:
-      - entry: {$include: merge-metadata.py}
-        entryname: merge-metadata.py
-baseCommand: [python3, merge-metadata.py]
+    listing: |
+          ${
+          var i = 0;
+          var b = 1;
+          var out = [];
+          for (; i < inputs.metadata.length; i++) {
+            var block = [];
+            var sub = [];
+            for (; i < (b*150) && i < inputs.metadata.length; i++) {
+              block.push(inputs.metadata[i]);
+              sub.push(inputs.subjects[i]);
+            }
+            out.push({
+              entryname: "block"+b,
+              entry: JSON.stringify(block)
+            });
+            out.push({
+              entryname: "subs"+b,
+              entry: JSON.stringify(sub)
+            });
+            b++;
+          }
+          return out;
+          }
+baseCommand: python