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eb3705f
Add single unit modules for downstream analysis
cavenel Mar 13, 2026
1199021
Remove unused modules
cavenel Mar 13, 2026
9e1ca1d
Temporary remove integration of samples
cavenel Mar 13, 2026
7cff804
Remove intermediate sdata exports
cavenel Mar 13, 2026
a1bc71e
Add Apple ARM64 compatibility for Python scripts
fasterius Mar 14, 2026
8d7d722
Remove unused Python f-string
fasterius Mar 14, 2026
a18f386
Remove unused `X_dense` object
fasterius Mar 14, 2026
cba348f
Disable Quarto echo globally
fasterius Mar 14, 2026
681e741
Plot QC metrics distributions in tabset
fasterius Mar 14, 2026
94ebcd9
Don't show warnings globally in Quarto report
fasterius Mar 14, 2026
5f1497e
Plot spatial QC in tabsets
fasterius Mar 14, 2026
c261780
Publish plots from report
fasterius Mar 14, 2026
b91638f
Add function to save figures from report
fasterius Mar 14, 2026
0614a47
Remove data loading print statements
fasterius Mar 14, 2026
2a23d51
Use lightbox for all report figures
fasterius Mar 14, 2026
3db4029
Fix HVG figure size; prettify HVG output
fasterius Mar 14, 2026
8e65d7a
Prettify PCA output
fasterius Mar 14, 2026
e06c418
Plot UMAPs in a tabset
fasterius Mar 14, 2026
0fa8b8b
Prettify cluster assignment/distribution plots
fasterius Mar 14, 2026
fed6fa4
Fix header capitalisation
fasterius Mar 14, 2026
fdd3fa7
Save top marker per clusters using common function
fasterius Mar 14, 2026
6774e2f
Prettify differential expression section
fasterius Mar 14, 2026
69987ca
Prettify spatial section
fasterius Mar 15, 2026
1664e23
Display top SVGs using a data frame
fasterius Mar 15, 2026
053179c
Show top SVGs in tabset
fasterius Mar 15, 2026
cb4ecbb
Prettify summary section
fasterius Mar 15, 2026
072aa43
Use a dataframe to print package versions
fasterius Mar 15, 2026
e836c07
Guard tabset creation with conditionals
fasterius Mar 15, 2026
2e09474
Use a data frame for cluster statistics table
fasterius Mar 15, 2026
9860d12
Create re-usable function for displaying tables
fasterius Mar 15, 2026
5f6513f
Use common table function for all tables
fasterius Mar 15, 2026
aa133f4
Remove hover from table headers
fasterius Mar 16, 2026
c3f6041
Remove unused module import
fasterius Mar 16, 2026
05c2043
Include tabset div creation in common function
fasterius Mar 16, 2026
487533e
Remove redundant figure size global setting
fasterius Mar 16, 2026
ff8bed5
Remove unused scripts/reports and related code
fasterius Mar 17, 2026
0c6a336
Formatting and harmonisation
fasterius Mar 17, 2026
ab74b3c
Pass `n_top_svgs` parameter to report
fasterius Mar 17, 2026
885cb96
Fix `versions` topic for modules
fasterius Mar 17, 2026
d6030ef
Add missing module parameters
fasterius Mar 18, 2026
11b7619
Add additional module parameters; harmonisation
fasterius Mar 19, 2026
9c5d982
Remove `umap_n_components` in favour of defaults
fasterius Mar 19, 2026
7c6b488
Change `rank_genes_method` default to `wilcoxon`
fasterius Mar 19, 2026
78c7f7c
Use template for SDATA_MERGE` module
fasterius Mar 19, 2026
e8e87ab
Remove empty modules
fasterius Mar 19, 2026
8956823
Add `scanpy/scanorama` module
fasterius Mar 20, 2026
a2904c7
Add existing modules to aggregation subworkflow
fasterius Mar 20, 2026
11db057
Add integration mode to `SDATA_UPDATE`
fasterius Mar 21, 2026
145ec23
Add integration report back into the workflow
fasterius Mar 21, 2026
25aa274
Rename modules for clarify; harmonisation
fasterius Mar 21, 2026
2961d3c
Remove manual QC metric calculation function
fasterius Mar 21, 2026
688f5a3
Add `[sample,cluster]_col` as report parameters
fasterius Mar 21, 2026
191d2d0
Fix module publishing
fasterius Mar 21, 2026
ff084fc
Move `SDATA_MERGE` to root workflow; clarify names
fasterius Mar 21, 2026
e989523
Add missing module tags
fasterius Mar 21, 2026
06f9598
Add functionality for choosing integration method
fasterius Mar 21, 2026
1e4740f
Add Harmony integration
fasterius Mar 22, 2026
9f5621c
Make sure `var` is correctly merged with Scanorama
fasterius Mar 22, 2026
98002b3
Remove unused parameter
fasterius Mar 22, 2026
29d23f8
Reduce Scanpy verbosity in report
fasterius Mar 22, 2026
0d8dca0
Remove cluster name-related parameters
fasterius Mar 22, 2026
0e4a05a
Change merging/integration default prefixes
fasterius Mar 23, 2026
b0e00fa
Move `SDATA_TO_LEGACY_ANNDATA` to root workflow
fasterius Mar 23, 2026
5990509
Separate DOWNSTREAM subworkflow into parts
fasterius Mar 23, 2026
5adb15e
Harmonise language to American English spelling
fasterius Mar 24, 2026
d42740d
Update template structure for squidpy modules
cavenel Mar 24, 2026
36a2232
Harmonise and add tests for Scanpy modules
fasterius Mar 25, 2026
c8cd7ce
Update pipeline-level tests
fasterius Mar 26, 2026
691b8af
Add tests for SDATA modules
fasterius Mar 26, 2026
f817d40
Add tests for Squidpy modules
cavenel Mar 26, 2026
b76f358
Add tests for SQUIDPY neighbors/autocorr modules
fasterius Mar 26, 2026
926451a
Update snapshots to see fails cross-platform
fasterius Mar 26, 2026
99d0d89
Remove obsolete snapshots
cavenel Mar 26, 2026
7554263
Update Scanpy modules to use `nft-anndata` testing
fasterius Mar 26, 2026
25c28ec
Merge branch 'dev' into separate-scripts
fasterius Mar 26, 2026
93382fc
Update changelog
fasterius Mar 26, 2026
5dfcad7
Fix end of files
fasterius Mar 26, 2026
65daa0e
Integrate data by default
fasterius Mar 26, 2026
3c1764e
Add missing empty channels when not integrating
fasterius Mar 26, 2026
b6c64e8
Add missing output data
fasterius Mar 26, 2026
f491423
Update Squidpy modules to use `nft-anndata` testing
cavenel Mar 26, 2026
21b8065
Remove obsolete snapshot
cavenel Mar 26, 2026
38abefe
Update sdata modules to use `nft-anndata` testing when possible
cavenel Mar 26, 2026
378a6e4
Update remaining Scanpy modules to use `nft-anndata` testing
cavenel Mar 26, 2026
7fda1cf
Use only names of files from zarr objects
cavenel Mar 26, 2026
cedc5c2
Use only names of files from zarr objects
cavenel Mar 27, 2026
84fd5e7
Publish spatial autocorrelation gene results
fasterius Mar 27, 2026
206d7f4
Count lines of SVG output instead of snapshotting
fasterius Mar 27, 2026
cfaf7b3
Fix erroneously empty channel
fasterius Mar 27, 2026
1430381
Update pipeline-level tests
fasterius Mar 27, 2026
a5e3c42
Remove HVG fallback; add Cell Ranger flavour test
fasterius Mar 27, 2026
b6b1c1f
Disallow `seurat_v3` and `seurat_v3_paper` for HVG
fasterius Mar 27, 2026
1f39241
Ignore additional outputs for pipeline snapshots
fasterius Mar 27, 2026
a7a202f
Change `neighbors_n_pcs` to be an integer param
fasterius Mar 27, 2026
f75bd94
Add missing `n_pcs` change to tests
fasterius Mar 27, 2026
979c23f
Update pipeline-level snapshots
fasterius Mar 28, 2026
ce2de99
Convert `normalize_target_sum` param to integer
fasterius Mar 28, 2026
4908a09
Add missing log1p setup for PCA testing
fasterius Mar 28, 2026
82aa197
Fail PCA when HVGs missing + highly_variable true
fasterius Mar 28, 2026
7f6e653
Fix `normalize_target_sum` default parameter value
fasterius Mar 28, 2026
bd75aaf
Remove handling of few genes in HVG selection
fasterius Mar 28, 2026
b00c49a
Sort `stable_name` test output list
fasterius Mar 28, 2026
7c2e04b
Add AnnData YAML checks for pipeline-level tests
fasterius Mar 28, 2026
d5fe751
Update pipeline-level snapshots
fasterius Mar 28, 2026
f904dbe
Add missing HVG selection in tests
fasterius Mar 29, 2026
2c357ec
Ignore additional files in pipeline-level snapshot
fasterius Mar 29, 2026
4ce8279
Update pipeline-level snapshots
fasterius Mar 29, 2026
e2e8df0
Update to `nft-anndata` version `0.4.1`
fasterius Mar 29, 2026
20e957a
Update module snapshots
fasterius Mar 30, 2026
1b0fb9a
Update pipeline-level snapshots
fasterius Mar 30, 2026
547f010
Add `skip_downstream` parameter
fasterius Mar 30, 2026
ee462c9
Harmonise output naming across modules
fasterius Mar 30, 2026
d65b04d
Add missing `.collect()` at sdata merge step
fasterius Mar 30, 2026
56c711d
Move Zarr testing into separate snapshot
fasterius Mar 30, 2026
c408734
Always merge sdata
fasterius Mar 30, 2026
9f1a75c
Update pipeline-level snapshots
fasterius Mar 30, 2026
2421e72
Fix test data links
fasterius Mar 30, 2026
fc4a378
Update SDATA modules with new test dataset
fasterius Mar 30, 2026
ff9b7b8
Fix missing H5AD file publishing
fasterius Mar 30, 2026
b27eb93
Add names to downstream snapshot to troubleshoot
fasterius Mar 31, 2026
aecbfdd
Sort input samples before merging
fasterius Mar 31, 2026
1715d10
Add file name to downstream H5AD snapshots
fasterius Mar 31, 2026
2160ea3
Remove `sdata_merged` from integration outputs
fasterius Mar 31, 2026
08b6b8a
Rename integration parameter to `integrate_data`
fasterius Mar 31, 2026
25e7a97
Sort inputs where applicable for snapshot ordering
fasterius Mar 31, 2026
9e4c250
Sort AnnData outputs in downstream pipeline test
fasterius Mar 31, 2026
6a6d6c5
Sort AnnData outputs in all pipeline tests
fasterius Mar 31, 2026
f4e518f
Fix sorting in Harmony/Scanorama modules
fasterius Mar 31, 2026
cc1f91c
Remove leftover pipeline-level test parsing
fasterius Mar 31, 2026
b9794d5
Streamline integration module imports
fasterius Mar 31, 2026
a9b4bed
Move `ad.concat` into its own ADATA_MERGE module
fasterius Apr 1, 2026
d329fe0
Fix missing integration `.obs` cols in final sdata
fasterius Apr 1, 2026
975f71b
Fix merge module output names
fasterius Apr 1, 2026
dd9da94
Fix default pipeline test adata parsing
fasterius Apr 1, 2026
b4ca7b6
Update pipeline-level snapshots
fasterius Apr 1, 2026
103e80d
Harmonise and add missing module tests
fasterius Apr 1, 2026
2d9e1d6
Harmonise leftover SDATA modules
fasterius Apr 1, 2026
e19ba20
Use real sample IDs for `meta.id` in module tests
fasterius Apr 1, 2026
febfc8f
Remove fallback for `sdata.table` name
fasterius Apr 1, 2026
9470913
Add additional params to ADATA_MERGE module
fasterius Apr 2, 2026
84712cb
Add note on HD test data for READ_VISIUM module
fasterius Apr 2, 2026
a6d16b7
Module harmonisation and clean-up
fasterius Apr 2, 2026
56b883c
Optimise SCANPY_FILTER modules
fasterius Apr 2, 2026
02c9f77
Remove SCANPY_FILTER fallback
fasterius Apr 2, 2026
82694ea
Harmonise SCANPY_CALCULATE_QC_METRICS module
fasterius Apr 2, 2026
51bf335
Fix ADATA_MERGE-dependent module tests
fasterius Apr 2, 2026
8adcdcf
Add testing of spatial AnnData for `SCANPY_FILTER`
fasterius Apr 2, 2026
d3844f4
Add additional variables / tests to SCANPY_HARMONY
fasterius Apr 5, 2026
15bc210
Add more variables and tests to SCANPY_SCANORAMA
fasterius Apr 5, 2026
0239be3
Harmonise + optimise SCANPY_HIGHLY_VARIABLE_GENES
fasterius Apr 5, 2026
90fed22
Harmonise SCANPY_LEIDEN
fasterius Apr 5, 2026
84b8e1b
Harmonise SCANPY_LOG1P
fasterius Apr 5, 2026
1a181d1
Harmonise SCANPY_NEIGHBORS
fasterius Apr 5, 2026
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3 changes: 2 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,14 @@ pipeline development was moved to nf-core and NBIS. The pipeline has undergone
several iterations regarding its functionality and content; there are a
significant number of changes, of which not all are listed here. In summary, the
pipeline contains best-practice processing and analyses of pre- and post-Space
Ranger-processed data, including quality controls, normalisation, dimensionality
Ranger-processed data, including quality controls, normalization, dimensionality
reduction, clustering, differential expression testing as well as output files
compatible with further downstream analyses and/or exploration in _e.g._
[TissUUmaps](https://tissuumaps.github.io/) or bespoke user code.

### `Added`

- Separate reports into separate scripts [[#137](https://github.com/nf-core/spatialvi/pull/137)]
- Use topic channels for software versions [[#133](https://github.com/nf-core/spatialvi/pull/133)]
- Make the main spatial Docker image work with Seqera Containers [[#127](https://github.com/nf-core/spatialvi/pull/127)]
- Fix 'dir' handling for cloud file systems [[#122](https://github.com/nf-core/spatialvi/pull/122)]
Expand Down
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ the following steps:

0. Raw data processing with Space Ranger (optional)
1. Quality controls and filtering
2. Normalisation
2. Normalization
3. Dimensionality reduction and clustering
4. Differential gene expression testing

Expand Down
163 changes: 0 additions & 163 deletions bin/clustering.qmd

This file was deleted.

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