WIP: remove preprocessing pipelines#823
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jameshadfield wants to merge 4 commits intomove-filterfrom
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Starts to reorganize the workflow such that we only need the sequence index when subsampling with priorities and we only filter after the subsampling, alignment, and mask steps. Related to #810
These should be small enough, it isn't worth the extra effort/complexity to compress.
jameshadfield
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This change is a companion to nextstrain/ncov#823 which removed the preprocessing pipelines.
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Closing this PR since @jameshadfield and I cherry-picked its single new commit onto the original move-filter PR (9abad2a). |
tsibley
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Use aligned sequences as the aligned sequences input, rather than pass off unaligned sequences as the aligned sequences input. This should be inconsequential to workflow behaviour or results, but it makes the config a bit more straightforward and less confusing. In a quick dig thru history, it seems like ncov-ingest's aligned.fasta.xz was not _quite_ available when we first switched our profiles to use an "aligned" input instead of a "sequences" input. The original use of "aligned" with unaligned sequences was driven by run time concerns and related to the move of the filtering step after the subsampling step and move of the "preprocess" steps from this workflow (ncov) to ncov-ingest.¹ ¹ <#814> <#823>
tsibley
added a commit
that referenced
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Apr 6, 2023
Use aligned sequences as the aligned sequences input, rather than pass off unaligned sequences as the aligned sequences input. This should be inconsequential to workflow behaviour or results, but it makes the config a bit more straightforward and less confusing. In a quick dig thru history, it seems like ncov-ingest's aligned.fasta.xz was not _quite_ available when we first switched our profiles to use an "aligned" input instead of a "sequences" input. The original use of "aligned" with unaligned sequences was driven by run time concerns and related to the move of the filtering step after the subsampling step and move of the "preprocess" steps from this workflow (ncov) to ncov-ingest.¹ Resolves <#1054>. ¹ <#814> <#823>
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WIP
config.uploadtrigger_phylogenetic_rebuildgisaid/rebuild/open/rebuild. This is Update repository dispatch triggers ncov-ingest#255