- if s.name() == ".":
- for f in s.all_files():
- result = prog.match(f.name())
- print f.name()
- if result != None:
- p = [{}, {}]
- p[0]["reader"] = s.file(f)
- p[1]["reader"] = s.file(prog.group(1) + "_2.fastq")
-
-print manifest_text
-
-#arvados.current_task().set_output(put_manifest(manifest_text))
+ for f in s.all_files():
+ name_pieces = prog.match(f.name())
+ if name_pieces is not None:
+ if s.name() != ".":
+ # The downstream tool (run-command) only iterates over the top
+ # level of directories so if there are fastq files in
+ # directories in the input, the choice is either to forget
+ # there are directories (which might lead to name conflicts) or
+ # just fail.
+ print >>sys.stderr, "fastq must be at the root of the collection"
+ sys.exit(1)
+
+ p = None
+ if name_pieces.group(2) is not None:
+ if name_pieces.group(2) == "_1":
+ p = [{}, {}]
+ p[0]["reader"] = s.files()[name_pieces.group(0)]
+ p[1]["reader"] = s.files()[name_pieces.group(1) + "_2.fastq" + (name_pieces.group(3) if name_pieces.group(3) else '')]
+ else:
+ p = [{}]
+ p[0]["reader"] = s.files()[name_pieces.group(0)]
+
+ if p is not None:
+ for i in xrange(0, len(p)):
+ m = p[i]["reader"].as_manifest().split()
+ m[0] = "./_" + str(piece)
+ manifest_list.append(m)
+ piece += 1
+
+manifest_text = "\n".join(" ".join(m) for m in manifest_list) + "\n"
+
+arvados.current_task().set_output(manifest_text)