Linx neo-epitope file(tumor-id.linx.neoepitope.tsv) not found

hartwigmedical / hmftools

Various algorithms for analysing genomics data

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Linx neo-epitope file(tumor-id.linx.neoepitope.tsv) not found #429

Closed YingYa closed 1 year ago

YingYa commented 1 year ago

I am running neo (v1.0.1), and get the following warning: Linx neo-epitope file(tumor-id.linx.neoepitope.tsv) not found.

The neo-epitope file generated from Linx (v1.23.6) is named tumor-id.linx.neo_epitope.tsv, and is CSV format not TSV format.

After following processing, the neo could run without warning: csvtk csv2tab /path/to/linx/tumor-id.linx.neo_epitope.tsv > /path/to/linx/tumor-id.linx.neoepitope.tsv

charlesshale commented 1 year ago

Linx will write TSV output from v1.24 onwards, due for release shortly