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multi-sample lineage tasks #368

Merged
merged 9 commits into from
Oct 1, 2021
Merged

multi-sample lineage tasks #368

merged 9 commits into from
Oct 1, 2021

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dpark01
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@dpark01 dpark01 commented Sep 27, 2021

Add multi-sample lineage calling support to tasks pangolin_many_samples and nextclade_many_samples in tasks_sarscov2.wdl. Update sarscov2_batch_relineage workflow to call multi-sample tasks instead of scattering across every genome. Update sarscov2_illumina_full to use sarscov2_batch_relineage instead of scattering sarscov2_lineages across every genome.

Do not merge yet: sarscov2_batch_relineage seems to be working okay so far, but sarscov2_illumina_full changes have not yet been vetted, esp with column order changes. Test run here. Check outputs with both GP teams before merge.

@dpark01 dpark01 marked this pull request as ready for review October 1, 2021 17:49
@dpark01 dpark01 merged commit 687f21f into master Oct 1, 2021
@dpark01 dpark01 deleted the dp-lineages branch October 1, 2021 19:43
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