Open messersc opened 7 years ago
At the moment,
biomedsheets/io_tsv/base.py allows 'WES', 'WGS', 'Panel_seq', 'mRNA_seq', 'total_RNA_seq'.
biomedsheets/io_tsv/base.py
'WES', 'WGS', 'Panel_seq', 'mRNA_seq', 'total_RNA_seq'
However, biomedsheets/data/std_fields.json defines the following:
biomedsheets/data/std_fields.json
"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.
Some additional protocols should perhaps be added:
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:The former is the one that is used by cubi_pipeline to parse the tsv. These definitions should be unified.