Add tool+cwl spec to flatten a list of lists of files

nlppln/commands/flatten_list.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+import click
+import json
+import codecs
+import itertools
+
+
+@click.command()
+def command():
+    with codecs.open('files.json', encoding='utf-8') as data:
+        list_of_lists = json.load(data)
+
+    flattened = list(itertools.chain(*list_of_lists))
+
+    stdout_text = click.get_text_stream('stdout')
+    stdout_text.write(json.dumps({'out_files': flattened}))
+
+
+if __name__ == '__main__':
+    command()

nlppln/cwl/flatten-list.cwl

@@ -0,0 +1,27 @@
+#!/usr/bin/env cwlrunner
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: ["python", "-m", "nlppln.commands.flatten_list"]
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: files.json
+        entry: $(JSON.stringify(inputs.list))
+
+inputs:
+  list:
+    type:
+      type: array
+      items:
+        type: array
+        items: File
+
+
+stdout: cwl.output.json
+
+outputs:
+  out_files:
+    type: File[]
+    outputBinding:
+      glob: "*"