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