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Improvement Description
Now that we have a brand-new unified view type for SE and PE fastq formats, fastq_stats_single and fastq_stats_paired could be merged into a single action. See: qiime2/q2-types#245
and here for an open PR where this unified view type is utilized: qiime2/q2-quality-control#52
Current Behavior
fastq_stats_single and fastq_stats_paired exist as separate visualizers. I am excited for these new visualizers! We have an opportunity to merge these into one before they area released to make use more straightforward.
Proposed Behavior
Merge these visualizers into one fastq_stats visualizer. This can probably be done by:
changing the view type here to CasavaOneEightSingleLanePerSampleDirFmt (that format has a new manifest property so afaik this line should still work but needs testing)
instead of this if statement you could then just check if the manifest has a reverse column.
in plugin_setup.py you would register a union type as the input type. E.g., instead of specifying SampleData[PairedEndSequencesWithQuality] as seen here you would do SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]
Then just cleaning up the docs, tests etc to use the unified action. (I may be missing a few other steps, but the above should be the gist of the main changes I think)
The text was updated successfully, but these errors were encountered:
Improvement Description
Now that we have a brand-new unified view type for SE and PE fastq formats, fastq_stats_single and fastq_stats_paired could be merged into a single action. See:
qiime2/q2-types#245
and here for an open PR where this unified view type is utilized:
qiime2/q2-quality-control#52
Current Behavior
fastq_stats_single and fastq_stats_paired exist as separate visualizers. I am excited for these new visualizers! We have an opportunity to merge these into one before they area released to make use more straightforward.
Proposed Behavior
Merge these visualizers into one
fastq_stats
visualizer. This can probably be done by:CasavaOneEightSingleLanePerSampleDirFmt
(that format has a newmanifest
property so afaik this line should still work but needs testing)reverse
column.plugin_setup.py
you would register a union type as the input type. E.g., instead of specifyingSampleData[PairedEndSequencesWithQuality]
as seen here you would doSampleData[SequencesWithQuality | PairedEndSequencesWithQuality]
Then just cleaning up the docs, tests etc to use the unified action. (I may be missing a few other steps, but the above should be the gist of the main changes I think)
The text was updated successfully, but these errors were encountered: