import os
import pandas as pd

sa = pd.read_csv("sample_annotation_relative.tsv", sep='\t')

for key in ['RNA_BAM_FILE', 'DNA_VCF_FILE', 'GENE_COUNTS_FILE']:
    if key not in sa.columns:
        continue
    sa[key] = [os.path.realpath(x) if not pd.isna(x) else x for x in sa[key] if x]

sa.to_csv("sample_annotation.tsv", sep='\t', index=False)