[Freyja] Remove lineage file if not SARS-CoV-2

[Michal-Babins]

🆒

📌 Explain the Request

Remove SARS-CoV-2 lineage file if pathogen is not SARS-CoV-2. As of Freyja release v1.5.2, the pathogen flag is exposed and this leads to other allowed pathogens outside of SARS-CoV-2. For other pathogens we don't want the pangolineage.

[AndrewLangvt]

@Michal-Babins can you provide a bit more context here... where does the lineage file come from/land if a non-SC2 pathogen is prescribed by the user?

[Michal-Babins]

Within the freyja task, the default behavior is to pass in this freyja_lineage_metadata file, however this is specifically for sars-cov-2, newer versions of freyja support other pathogens. We only want this file to be passed in to here

public_health_bioinformatics/tasks/taxon_id/freyja/task_freyja.wdl

Line 80 in c6d238b

~{"--meta " + freyja_lineage_metadata} \

and here

public_health_bioinformatics/tasks/taxon_id/freyja/task_freyja.wdl

Line 95 in c6d238b

~{'--meta ' + freyja_lineage_metadata} \

. Other pathogens just use barcodes so this flag is not needed for anything other than sars-cov-2.