Move stage definition to workflow - #98
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Aratz
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August 24, 2026 09:13
maxkarlsson
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Looks very good to me 🎉
Some minor comments, just to remove a bloat test file.
Really appreciate your work on this 🙏
| sample_levels <- es_data$sample_aliases | ||
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| plot_data <- | ||
| extract_sample_qc_metrics( |
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A note for the future: This extraction function should be updated to fit the new data ingestion better. But that is something we should do in a future PR
| @@ -0,0 +1,3 @@ | |||
| amplicon_stages <- function() { | |||
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I don't understand why this file is needed 😮 I think we can do without it.
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We should be able to use get_es_workflow_stages("amplicon_demux") instead
| #' @return A nested named list of functions. | ||
| #' | ||
| #' @noRd | ||
| .amplicon_demux_extractors <- function() { |
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It is good that you moved these functions to their own file 👍
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This PR lets each workflow define its own stages. This is then used downstream to determine which files to expect and populate the es_data.
Description
Describe the change.
Fixes: PNA-3323
Type of change
How Has This Been Tested?
Unit tests were run
PR checklist:
Note
Medium Risk
Breaking public API:
register_es_data_workflow(),find_stage(),get_file_paths(), andextract_sample_qc_metrics()now require a stages argument, so extension packages and existing callers will fail until they pass a vocabulary.Overview
Breaking: pipeline stages are no longer package globals. Each workflow must register a
stagesfactory (all,pool,pxl_preference), stored ones_data$stagesand retrieved withget_es_workflow_stages().find_stage(),get_file_paths(), andextract_sample_qc_metrics()now take a requiredstagesargument (no default), so discovery cannot inherit another workflow’s vocabulary. PXL preference and pool-level QC routing come from that list; the collapse-shard QC filter only runs ifcollapseis inall.The built-in
amplicon_demuxfactories (extractors, report, stages) move toworkflow_amplicon_demux.R. Registration validates the vocabulary (subsets ofall, unique names, emptypoolallowed). Downstream callers and tests passes_data$stagesorget_es_workflow_stages("amplicon_demux").Reviewed by Cursor Bugbot for commit 21755e1. Bugbot is set up for automated code reviews on this repo. Configure here.