but this approach would limit the new output to ivar based workflows ⚠️
If we wanted to add this output to other workflows, like theiacov on Flu track or TheiaCoV_ONT, we would need to use the assembled_reads_percent WDL task from TheiaMeta and pass in BAM files.
My first suggestion would take less time to develop and would satisfy the request but the downside is that TheiaCoV_ONT, TheiaCoV_illumina_pe + Flu, TheiaCoV_Clearlabs users would lack this output.
Maybe there are other solutions I have not thought of 🤔 ?
We should discuss as a team and decide how to proceed. Also need to consider if we want this in the next release or a later release.
:books: Context
request from CDPH
:chart_with_upwards_trend: Desired Behavior
Add the percentage_mapped_reads output column to TheiaCoV workflows
:cool:
:pushpin: Explain the Request
A user requested that the
percentage_mapped_readswhich appears in TheiaMeta....theiameta workflow output: https://github.com/theiagen/public_health_bioinformatics/blob/74c12d3bbced7177638fdfdc50c56f8bc40a0f5a/workflows/theiameta/wf_theiameta_illumina_pe.wdl#L266
theiameta task that generates this output: https://github.com/theiagen/public_health_bioinformatics/blob/74c12d3bbced7177638fdfdc50c56f8bc40a0f5a/tasks/utilities/data_handling/task_parse_mapping.wdl#L206
...be added to TheiaCoV workflows. I'm thinking we could add this to iVar based workflows (theiacov_illumina_pe, theiacov_illumina_se) pretty easily by parsing this information out of the samtools flagstat file: https://github.com/theiagen/public_health_bioinformatics/blob/74c12d3bbced7177638fdfdc50c56f8bc40a0f5a/tasks/quality_control/basic_statistics/task_assembly_metrics.wdl#L20
but this approach would limit the new output to ivar based workflows ⚠️
If we wanted to add this output to other workflows, like theiacov on Flu track or TheiaCoV_ONT, we would need to use the
assembled_reads_percentWDL task from TheiaMeta and pass in BAM files.My first suggestion would take less time to develop and would satisfy the request but the downside is that TheiaCoV_ONT, TheiaCoV_illumina_pe + Flu, TheiaCoV_Clearlabs users would lack this output.
Maybe there are other solutions I have not thought of 🤔 ?
We should discuss as a team and decide how to proceed. Also need to consider if we want this in the next release or a later release.
:books: Context
request from CDPH
:chart_with_upwards_trend: Desired Behavior
Add the
percentage_mapped_readsoutput column to TheiaCoV workflows:information_source: Additional Information