From 04ce6471338c42d2bc792c32357f1c18267d52ac Mon Sep 17 00:00:00 2001 From: Davide Rambaldi Date: Mon, 8 May 2023 17:00:41 +0200 Subject: [PATCH] Do not resolve paths for bamfile and barcodes: In nextflow files are staged with soft links in a working directory. If you follow soft links you end up searching for cellsorted_ file in the input directory not in the working directory. With this fix we are able to call velocyto in a nextflow pipeline --- velocyto/commands/run.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/velocyto/commands/run.py b/velocyto/commands/run.py index b16ae2a..6b7236d 100644 --- a/velocyto/commands/run.py +++ b/velocyto/commands/run.py @@ -24,7 +24,7 @@ def id_generator(size: int=6, chars: str=string.ascii_uppercase + string.digits) file_okay=True, dir_okay=False, readable=True, - resolve_path=True)) + resolve_path=False)) @click.argument("gtffile", type=click.Path(exists=True, file_okay=True, @@ -36,7 +36,7 @@ def id_generator(size: int=6, chars: str=string.ascii_uppercase + string.digits) Cell barcodes should be specified in the bcfile as the `CB` tag for each read""", default=None, show_default=True, - type=click.Path(resolve_path=True, + type=click.Path(resolve_path=False, file_okay=True, dir_okay=False, readable=True))