New module: 10x Space Ranger #1945
Conversation
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For next time (I know you copied this from the CellRanger module so this isn't really anything to do with you @grst, but still I feel compelled to say) - please don't make MultiQC module code too clever 😅 I'm trying to tweak the General Stats header config and I'm spending ages going around in circles trying to find where the attributes are set - in which function, which file, which dict. It's really much better to have verbose repetitive code that is easy to read, standardised with other MultiQC modules, and trivial to customise on a per-column basis. Even though everyone's knee-jerk response to seeing repetitive code is to optimise into a function, everyone does it differently and it hinders customisation - it causes a lot of hassle. Rant / shouting into the void over... 😬 |
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Mostly looking good, going from the report - thanks for this! Quick thoughts:
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Hi @ewels, I agree with pretty much everything of your rant. I needed a lot of time myself to understand the logic of the Spaceranger module and was particularly unhappy with the way Mixture classes are used here -- I still figured it was the fastest way to get the job done to reuse the code. Regarding your specific feedback:
should be fixed
the problem is that the cellranger/spaceranger HTML reports do not report passes, only failures. So yes, we could mark them as passes, but we never get the full matrix, only the samples that have at least one failure and only the failures that appear in at least one sample show up in the table. I'd be inclined to leave it as-is, but happy to change it if you prefer.
I checked the JSON we extract from the spaceranger report and don't think any further downsampling is necessary. It's about 20 data points per sample. |
This reverts commit 73d8d71.
vladsavelyev
added
module: new
and removed
awaits-review
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
…po (MultiQC#2399) * When checking for git SHA, make sure we are not inside another git repository * [automated] Update CHANGELOG.md --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
* Violin plot export: use metric titles instead of IDs * Add Export button for table. Do not prefix violin ID, instead prefix table. * Violin save_data_file: use titles instead of metric ids as well * [automated] Update CHANGELOG.md * Fix * Fix linting * CSP * Wrap table buttons in .col-xs-12 too to add some bottom padding * Use Export as CSV wording * Fix the edge case * Fix the edge case - 2 --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
* Add option to place bar plot legend on the bottom * [automated] Update CHANGELOG.md * Update docs --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
…n table cells (MultiQC#2395) * Violin plot export: use metric titles instead of IDs * Add Export button for table. Do not prefix violin ID, instead prefix table. * Violin save_data_file: use titles instead of metric ids as well * [automated] Update CHANGELOG.md * Fix * Avoid in tables * Fix linting * Unnecessary nowrap * Use a small space span before suffix * [automated] Update CHANGELOG.md * Also replace with a space in case if modules set it * changelog * Fix linting * CSP * Update old class name in the old highcharts theme * Fix CSP --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
* Move multiqc_data.json export out of megaqc.py and into util_functions * Better error message * [automated] Update CHANGELOG.md * Keep script_path str --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Vlad Savelyev <vladislav.sav@gmail.com>
CHANGELOG.mdhas been updated--lintflag)docs/README.mdis updated with link to belowdocs/modulename.mdis createdself.add_section)Add a module for 10x Space Ranger.
Since the output reports are very similar (yet not identical) to the Cellranger reports, I started by copying the cellranger module.