Change the way lablog viralrecon checks about already downloaded references in refgenie

[jaimeozaez]

Currently, the way lablog_viralrecon checks if a reference has already been downloaded is by checking if the /data/ucct/bi/references/refgenie/alias/references.txt file contains that registered reference. In case refgenie does not work as expected, it might be the situation where there is some discrepancy between the references.txt file and the /data/ucct/bi/references/refgenie/genome_config.yaml file. Then, lablog viralrecon should use the genome_config.yaml file as the most reliable way to check the already downloaded references, instead of references.txt.

buisciii-tools/buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon

Line 324 in 464645b

echo -e "${ref}\tfasta\t${family}\t/data/ucct/bi/references/refgenie/alias/${family}/fasta/${ref}/${family}.fa" >> /data/ucct/bi/references/refgenie/alias/references.txt