Commit 0a324771 authored by Sam Nooij's avatar Sam Nooij
Browse files

Move/copy/link sample_sheet to data/raw

parent a4180b47
......@@ -355,7 +355,7 @@ def main():
if mode == "move":
print("Moving files from %s to %s" % (arguments.input, arguments.output))
move_file(input_dict["Sample_sheet"], Path(main_output / "data" / "Sample_sheet.yaml"))
move_file(input_dict["Sample_sheet"], Path(main_output / "data" / "raw" / "sample_sheet.yaml"))
for trimmed_file in input_dict["Trimmed_reads"]:
move_file(trimmed_file, Path(main_output / "data" / "raw" / "trimmed_reads" / trimmed_file.name))
......@@ -373,7 +373,7 @@ def main():
elif mode == "copy":
print("Copying files from %s to %s" % (arguments.input, arguments.output))
copy_file(input_dict["Sample_sheet"], Path(main_output / "data" / "raw"))
copy_file(input_dict["Sample_sheet"], Path(main_output / "data" / "raw" / "sample_sheet.yaml"))
for trimmed_file in input_dict["Trimmed_reads"]:
copy_file(trimmed_file, Path(main_output / "data" / "raw" / "trimmed_reads" / trimmed_file.name))
......@@ -391,7 +391,7 @@ def main():
elif mode == "link":
print("Creating symbolic links from %s to %s" % (arguments.input, arguments.output))
link_file(input_dict["Sample_sheet"], Path(main_output / "data" / "raw"))
link_file(input_dict["Sample_sheet"], Path(main_output / "data" / "raw" / "sample_sheet.yaml"))
for trimmed_file in input_dict["Trimmed_reads"]:
link_file(trimmed_file, Path(main_output / "data" / "raw" / "trimmed_reads" / trimmed_file.name))
......
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