Commit a25daaa7 authored by yy1533's avatar yy1533
Browse files

🍺 ST compatible. umi-start-position, bc-start-position, bc-seq-column in config

parent 07d64eab
......@@ -27,6 +27,9 @@ SAMPLE_TABLE = cook_sample_sheet(SAMPLE_TABLE_FPATH) # ''
# '/ifs/data/yanailab/refs/barcodes/barcodes_cel-seq_umis96.tab'
BC_INDEX_FPATH = config.get('BC_INDEX_FPATH', None)
BC_IDs_DEFAULT = config.get('BC_IDs_DEFAULT', None) # '1-96'
BC_SEQ_COLUMN = config.get('BC_SEQ_COLUMN', None)
UMI_START_POSITION = config.get('UMI_START_POSITION', None)
BC_START_POSITION = config.get('BC_START_POSITION', None)
UMI_LENGTH = config.get('UMI_LENGTH', None) # 6
BC_LENGTH = config.get('BC_LENGTH', None) # 6
......@@ -185,8 +188,12 @@ rule combo_demultiplexing:
itemr1,
itemr2,
"--bc-index {}".format(BC_INDEX_FPATH),
"--bc-seq-column {}".format(BC_SEQ_COLUMN),
"--bc-index-used {}".format(itembc),
"--min-bc-quality {}".format(FASTQ_QUAL_MIN_OF_BC),
"--umi-start-position {}".format(
UMI_START_POSITION),
"--bc-start-position {}".format(BC_START_POSITION),
"--umi-length {}".format(UMI_LENGTH),
"--bc-length {}".format(BC_LENGTH),
"--cut-length {}".format(CUT_LENGTH),
......
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