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Use spatialdata #67

Merged
merged 72 commits into from
Apr 12, 2024
Merged

Use spatialdata #67

merged 72 commits into from
Apr 12, 2024

Commits on Jan 31, 2024

  1. Use spatialdata zarr objects instead of AnnData 

    Replace all reads and writes with SpatialData zarr, and use a "legacy anndata" conversion function to add images and scales, in order to plot with scanpy.
    @cavenel
    cavenel committed Jan 31, 2024
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  2. Fix typo

    @cavenel
    cavenel committed Jan 31, 2024
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  3. Fix black and prettier

    @cavenel
    cavenel committed Jan 31, 2024
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Commits on Feb 12, 2024

  1. Update Conda environment and Dockerfile

    @fasterius
    fasterius committed Feb 12, 2024
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  2. Add QUARTONOTEBOOK nf-core module

    @fasterius
    fasterius committed Feb 12, 2024
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  3. Use QUARTONOTEBOOK module in pipeline

    @fasterius
    fasterius committed Feb 12, 2024
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  4. Remove old local modules

    @fasterius
    fasterius committed Feb 12, 2024
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  5. Update changelog

    @fasterius
    fasterius committed Feb 12, 2024
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  6. Remove XDG paths, which are now in QUARTONOTEBOOK

    @fasterius
    fasterius committed Feb 12, 2024
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  7. Lower test thresholds

    @fasterius
    fasterius committed Feb 12, 2024
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  8. Revert "Lower test thresholds" 

    This reverts commit fe7a7dc.

Lowering the test thresholds was part of troubleshooting the spatial DE
module, but did solve the issue.
    @fasterius
    fasterius committed Feb 12, 2024
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  9. Fix report module output names and paths

    @fasterius
    fasterius committed Feb 12, 2024
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  10. Update Conda environment

    @fasterius
    fasterius committed Feb 12, 2024
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Commits on Feb 20, 2024

  1. Template update for nf-core/tools version 2.13

    @nf-core-bot
    nf-core-bot committed Feb 20, 2024
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Commits on Feb 29, 2024

  1. Template update for nf-core/tools version 2.13.1

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    nf-core-bot committed Feb 29, 2024
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Commits on Mar 1, 2024

  1. Remove redundant environment specification

    @fasterius
    fasterius committed Mar 1, 2024
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  2. Update MultiQC module

    @fasterius
    fasterius committed Mar 1, 2024
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  3. Use Space Ranger output for MultiQC

    @fasterius
    fasterius committed Mar 1, 2024
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  4. Add missing MultiQC output documentation

    @fasterius
    fasterius committed Mar 1, 2024
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  5. Update changelog

    @fasterius
    fasterius committed Mar 1, 2024
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Commits on Mar 4, 2024

  1. Fix tables writing in SpatialData objects

    @cavenel
    cavenel committed Mar 4, 2024
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  2. Fix quarto formatting

    @cavenel
    cavenel committed Mar 4, 2024
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  3. Move from SpatialDE to Squidpy for SVG computation

    @cavenel
    cavenel committed Mar 4, 2024
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Commits on Mar 5, 2024

  1. Merge remote-tracking branch 'origin/dev' into use-spatialdata

    @fasterius
    fasterius committed Mar 5, 2024
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  2. Add util-subworkflows and move most lib/ content

    @fasterius
    fasterius committed Mar 5, 2024
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  3. Merge branch 'TEMPLATE' into template-updates

    @fasterius
    fasterius committed Mar 5, 2024
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  4. Add missing versions export for INPUT_CHECK

    @fasterius
    fasterius committed Mar 5, 2024
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  5. Add missing FastQC input to MultiQC

    @fasterius
    fasterius committed Mar 5, 2024
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  6. Update UNTAR module

    @fasterius
    fasterius committed Mar 5, 2024
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  7. Merge branch 'multiqc-spaceranger' into use-spatialdata

    @fasterius
    fasterius committed Mar 5, 2024
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  8. Merge branch 'template-updates' into use-spatialdata

    @fasterius
    fasterius committed Mar 5, 2024
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  9. Update nf-test with new downstream subworkflow

    @fasterius
    fasterius committed Mar 5, 2024
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Commits on Mar 6, 2024

  1. Merge branch 'quartonotebook' into use-spatialdata

    @fasterius
    fasterius committed Mar 6, 2024
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  2. Add missing Spaceranger MultiQC input

    @fasterius
    fasterius committed Mar 6, 2024
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  3. Fix notebook name and zarr/h5ad output patterns

    @fasterius
    fasterius committed Mar 6, 2024
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Commits on Mar 7, 2024

  1. Fix SVG report test assertions

    @fasterius
    fasterius committed Mar 7, 2024
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  2. Delete old spatial DE report

    @fasterius
    fasterius committed Mar 7, 2024
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  3. Fix publishing of AnnData object

    @fasterius
    fasterius committed Mar 7, 2024
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  4. Fix publishing of DEG CSV

    @fasterius
    fasterius committed Mar 7, 2024
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  5. Add testing of SpatialData output

    @fasterius
    fasterius committed Mar 7, 2024
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  6. Minor formatting

    @fasterius
    fasterius committed Mar 7, 2024
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  7. Update snapshots

    @fasterius
    fasterius committed Mar 7, 2024
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Commits on Mar 19, 2024

  1. Rename SVG to spatially variable genes

    @fasterius
    fasterius committed Mar 19, 2024
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  2. Remove st_ prefix from names/variables/etc.

    @fasterius
    fasterius committed Mar 19, 2024
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  3. Update snapshots

    @fasterius
    fasterius committed Mar 19, 2024
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Commits on Mar 20, 2024

  1. Update citations

    @fasterius
    fasterius committed Mar 20, 2024
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  2. Fix duplicate citation entries

    @fasterius
    fasterius committed Mar 20, 2024
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Commits on Mar 21, 2024

  1. Add pipeline logo to Quarto report ToCs

    @fasterius
    fasterius committed Mar 21, 2024
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Commits on Apr 2, 2024

  1. Downgrade Quarto to 1.3 due to figure formatting 

    Downgrade the Quarto version to 1.3 due to some odd interaction between
the Python figures and the `layout-ncol` Quarto chunk option in 1.4,
which made the figures come out horizontally squashed.
    @fasterius
    fasterius committed Apr 2, 2024
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  2. Update snapshots

    @fasterius
    fasterius committed Apr 2, 2024
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  3. Include SpatialData description in all outputs

    @cavenel
    cavenel committed Apr 2, 2024
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  4. Clean Spatially Variable Genes quarto markdown

    @cavenel
    cavenel committed Apr 2, 2024
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Commits on Apr 4, 2024

  1. Update changelog

    @fasterius
    fasterius committed Apr 4, 2024
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  2. Remove duplicate citation for SpatialData

    @fasterius
    fasterius committed Apr 4, 2024
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  3. Minor formatting

    @fasterius
    fasterius committed Apr 4, 2024
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  4. Update quartonotebook module

    @fasterius
    fasterius committed Apr 4, 2024
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  5. Update spaceranger/count module

    @fasterius
    fasterius committed Apr 4, 2024
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  6. Remove TODO

    @fasterius
    fasterius committed Apr 4, 2024
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Commits on Apr 12, 2024

  1. Update SpatialData to v0.1.2

    @cavenel
    cavenel committed Apr 12, 2024
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  2. Remove temporary fix for scanpy issue

    @cavenel
    cavenel committed Apr 12, 2024
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  3. Add back missing line in SVG quarto

    @cavenel
    cavenel committed Apr 12, 2024
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  4. Fix spelling of AnnData

    @cavenel
    cavenel committed Apr 12, 2024
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  5. Clean read_zarr local path

    @cavenel
    cavenel committed Apr 12, 2024
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  6. Fix qmd headers

    @cavenel
    cavenel committed Apr 12, 2024
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  7. Move degs/ output to data/ folder

    @fasterius
    fasterius committed Apr 12, 2024
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  8. Add fix for pip install in Dockerfile

    @fasterius
    fasterius committed Apr 12, 2024
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  9. Fix adata import order

    @cavenel
    cavenel committed Apr 12, 2024
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  10. Merge branch 'use-spatialdata' of https://github.com/nf-core/spatialt… 

    …ranscriptomics into use-spatialdata
    @cavenel
    cavenel committed Apr 12, 2024
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  11. Remove trailing whitespace

    @cavenel
    cavenel committed Apr 12, 2024
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  12. Export spatialdata_io version

    @fasterius
    fasterius committed Apr 12, 2024
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  13. Remove Conda profile for READ_DATA process

    @fasterius
    fasterius committed Apr 12, 2024
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  14. Update snapshots

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    fasterius committed Apr 12, 2024
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