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-rw-r--r--workflows/pangenome-generate/merge-metadata.cwl46
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