From 89ee3fda73417865fba724475873f7e3b50beff0 Mon Sep 17 00:00:00 2001 From: EddieLF Date: Thu, 1 Feb 2024 20:36:58 +1100 Subject: [PATCH] Change reference to 'library_type' to 'sequencing_library' --- metamist/parser/sample_file_map_parser.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/metamist/parser/sample_file_map_parser.py b/metamist/parser/sample_file_map_parser.py index 5bb7dc17d..4f0b233f4 100644 --- a/metamist/parser/sample_file_map_parser.py +++ b/metamist/parser/sample_file_map_parser.py @@ -17,7 +17,7 @@ SEQ_TYPE_COL_NAME = 'type' CHECKSUM_COL_NAME = 'checksum' SEQ_FACILITY_COL_NAME = 'sequencing_facility' -LIBRARY_TYPE_COL_NAME = 'sequencing_library' +SEQ_LIBRARY_COL_NAME = 'sequencing_library' READ_END_TYPE_COL_NAME = 'read_end_type' READ_LENGTH_COL_NAME = 'read_length' @@ -36,7 +36,7 @@ READS_COL_NAME: ['filename', 'filenames', 'files', 'file'], SEQ_TYPE_COL_NAME: ['type', 'types', 'sequencing type', 'sequencing_type'], SEQ_FACILITY_COL_NAME: ['facility', 'sequencing facility', 'sequencing_facility'], - LIBRARY_TYPE_COL_NAME: ['library', 'library_prep', 'library prep', 'library type', 'library_type', 'sequencing_library', 'sequencing library'], + SEQ_LIBRARY_COL_NAME: ['library', 'library_prep', 'library prep', 'library type', 'library_type', 'sequencing_library', 'sequencing library'], READ_END_TYPE_COL_NAME: ['read_end_type', 'read end type', 'read_end_types', 'read end types', 'end type', 'end_type', 'end_types', 'end types'], READ_LENGTH_COL_NAME: ['length', 'read length', 'read_length', 'read lengths', 'read_lengths'], CHECKSUM_COL_NAME: ['md5', 'checksum'], @@ -120,7 +120,7 @@ def __init__( # pylint: disable=too-many-arguments checksum_column=CHECKSUM_COL_NAME, seq_type_column=SEQ_TYPE_COL_NAME, seq_facility_column=SEQ_FACILITY_COL_NAME, - library_type_column=LIBRARY_TYPE_COL_NAME, + seq_library_column=SEQ_LIBRARY_COL_NAME, read_end_type_column=READ_END_TYPE_COL_NAME, read_length_column=READ_LENGTH_COL_NAME, default_sample_type=default_sample_type,