From 1e8a74d881e408003fe3fd9f9bce43571be1a3d0 Mon Sep 17 00:00:00 2001 From: Tianhao-Gu Date: Fri, 16 Aug 2024 14:53:06 -0500 Subject: [PATCH] include ids_to_files --- src/loaders/compute_tools/checkm2/checkm2.py | 3 ++- src/loaders/compute_tools/gtdb_tk/gtdb_tk.py | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/loaders/compute_tools/checkm2/checkm2.py b/src/loaders/compute_tools/checkm2/checkm2.py index a8c4765d..eeb14466 100644 --- a/src/loaders/compute_tools/checkm2/checkm2.py +++ b/src/loaders/compute_tools/checkm2/checkm2.py @@ -72,7 +72,8 @@ def _run_checkm2( metadata = {'tool': 'checkm2', 'version': '1.0.1', 'command': command, - 'reference_db': 'diamond_db ver unknown - saved copy in NERSC at global/cfs/cdirs/kbase/collections/libraries/checkm2/1.0.1/uniref100.KO.1.dmnd',} + 'reference_db': 'diamond_db ver unknown - saved copy in NERSC at global/cfs/cdirs/kbase/collections/libraries/checkm2/1.0.1/uniref100.KO.1.dmnd', + 'ids_to_files': ids_to_files} create_tool_metadata(output_dir, metadata) diff --git a/src/loaders/compute_tools/gtdb_tk/gtdb_tk.py b/src/loaders/compute_tools/gtdb_tk/gtdb_tk.py index a0c41bf8..dd857197 100644 --- a/src/loaders/compute_tools/gtdb_tk/gtdb_tk.py +++ b/src/loaders/compute_tools/gtdb_tk/gtdb_tk.py @@ -154,7 +154,8 @@ def _run_gtdb_tk( metadata = {'tool': 'gtdb_tk', 'version': '2.3.2', 'command': command, - 'reference_db': 'release214',} + 'reference_db': 'release214', + 'ids_to_files': ids_to_files} create_tool_metadata(output_dir, metadata)