Hardcoding in output name from Script_VOCAL_unified.R

[silenus092]

1. Even though we have the option to change the output name, the code inside is still hardcoded

   Script_VOCAL_unified.R \
       -s "vocal-alerts-samples-all.csv" \
       -c "vocal-alerts-clusters-summaries-all.csv"

   
   write_csv(vocal_samples_out,
           file = file.path("vocal-alerts-samples-all.csv"))

write_csv( vocal_list_clusters_properties_with_mutations, file = file.path("vocal-alerts-clusters-summaries-all.csv") )

Note: the  Script_VOCAL_unified.R is modified to be used  in next flow pipeline, so if you run the 

Script_VOCAL_unified.R \
    -f ${variants_with_phenotypes} \
    -s "vocal-alerts-samples-all.csv" \
    -c "vocal-alerts-clusters-summaries-all.csv" \
    -a "${metadata}" \
    --ecdc ${ecdc} \
    --bloom ${bloom} \
    --lineages ${lineages}

the output directory will be the same when you execute the command