From 7c36d6627a766c38058847053de208a7bb129edc Mon Sep 17 00:00:00 2001 From: sepro Date: Thu, 1 Dec 2016 10:55:15 +0100 Subject: [PATCH] switched keep intermediate to remove-intermediate, to make it a consious descicion to remove the intermediate files --- run.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/run.py b/run.py index 12aceef..d48de88 100755 --- a/run.py +++ b/run.py @@ -107,7 +107,7 @@ def run_pipeline(args): parser.add_argument('--skip-orthofinder', dest='orthofinder', action='store_false', help='add --skip-orthofinder to skip the orthology detection') parser.add_argument('--skip-mcl-families', dest='mcl_families', action='store_false', help='add --skip-mcl to skip clustering blast with MCL') - parser.add_argument('--keep-intermediate', dest='keep_intermediate', action='store_true', help='add --keep-intermediate to prevent the pipeline from removing finished steps') + parser.add_argument('--remove-intermediate', dest='keep_intermediate', action='store_false', help='add --remove-intermediate to clear trimmomatic and tophat files after completing those steps') parser.add_argument('--disable-log', dest='enable_log', action='store_false', help='add --disable-log to disable writing additional statistics.') @@ -129,6 +129,7 @@ def run_pipeline(args): parser.set_defaults(orthofinder=True) parser.set_defaults(mcl_families=True) + parser.set_defaults(keep_intermediate=True) parser.set_defaults(enable_log=True) # Parse arguments and start pipeline