search

bihealth / biomedsheets

:books: JSON/TSV sample sheets for biomedical experiments
https://biomedsheets.readthedocs.io/en/master
3 stars 4 forks source link

Discrepancy in possible values for libraryType #10

Open messersc opened 7 years ago

messersc commented 7 years ago

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 5 years ago

Some additional protocols should perhaps be added: