theiagen / public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
https://public-health-viral-genomics-theiagen.readthedocs.io/
GNU Affero General Public License v3.0
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s_gene_percent_coverage float and percent_gene_coverage file for ClearLabs and ONT #129

Closed kapsakcj closed 2 years ago

kapsakcj commented 2 years ago

not properly calculated.

Need to remove 2 outputs from 2 workflows before creating v2.1.0 release

kapsakcj commented 2 years ago

Actually, no need to remove the outputs, we just need to set a mindepth input param and default value (20?) here at the workflow level:

https://github.com/theiagen/public_health_viral_genomics/blob/7c5f0c0fc8021e4ae6866ce8738346138e2837ce/workflows/wf_theiacov_clearlabs.wdl#L15

and ONT:

https://github.com/theiagen/public_health_viral_genomics/blob/7c5f0c0fc8021e4ae6866ce8738346138e2837ce/workflows/wf_theiacov_ont.wdl#L15

Then will have to feed in the new input parameter (min_depth) into the relevant tasks:

kapsakcj commented 2 years ago

Fixed in #131