diff --git a/bio/refgenie/test/Snakefile b/bio/refgenie/test/Snakefile index 095658c7fae..6767a71a54c 100644 --- a/bio/refgenie/test/Snakefile +++ b/bio/refgenie/test/Snakefile @@ -9,3 +9,15 @@ rule obtain_asset: tag="default" wrapper: "master/bio/refgenie" + +rule obtain_large_asset: + output: + # the name refers to the refgenie seek key (see attributes on http://refgenomes.databio.org) + star_index=directory("refs/star_index/hg38/star_index") + # Multiple outputs/seek keys are possible here. + params: + genome="hg38", + asset="star_index", + tag="default" + wrapper: + "master/bio/refgenie" diff --git a/bio/refgenie/wrapper.py b/bio/refgenie/wrapper.py index cdb36644397..3594085776a 100644 --- a/bio/refgenie/wrapper.py +++ b/bio/refgenie/wrapper.py @@ -15,7 +15,8 @@ rgc = refgenconf.RefGenConf(conf_path, writable=True) # pull asset if necessary -gat, archive_data, server_url = rgc.pull(genome, asset, tag, force=False) +# BUG Times out when pulling large assets +gat, archive_data, server_url = rgc.pull(genome, asset, tag, force=False, force_large=True) for seek_key, out in snakemake.output.items(): path = rgc.seek(genome, asset, tag_name=tag, seek_key=seek_key, strict_exists=True)