Discrepancy in possible values for libraryType
messersc opened this issue · comments
Clemens Messerschmidt commented
At the moment,
biomedsheets/io_tsv/base.py
allows
'WES', 'WGS', 'Panel_seq', 'mRNA_seq', 'total_RNA_seq'
.
However, biomedsheets/data/std_fields.json
defines the following:
"libraryType": {
"docs": "Rough classificiation of the library type",
"key": "libraryType",
"type": "enum",
"choices": [
"Panel-seq",
"WES",
"WGS",
"mRNA-seq",
"tRNA-seq",
"other"
]
},
The former is the one that is used by cubi_pipeline to parse the tsv. These definitions should be unified.
ericblanc20 commented
Some additional protocols should perhaps be added:
- ribodeplRNA_seq: ribodepletion/zeroribo RNA sequencing
- miRNA_seq: microRNA sequencing
- nascentRNA_seq: Global Run On (GRO-seq) sequencing
- others?