Code

Use spatialdata#67

Code

Merged

fasterius merged 72 commits intodevnf-core/spatialvi:devfrom use-spatialdatanf-core/spatialvi:use-spatialdataCopy head branch name to clipboardApr 12, 2024

+3,756-1,915

Commits

Commits on Jan 31, 2024

• Use spatialdata zarr objects instead of AnnData

  Show description for e13cf66
  cavenel

  committed
  e13cf66

• Fix typo

  cavenel

  committed
  d866f37

• Fix black and prettier

  cavenel

  committed
  aec833f

Commits on Feb 12, 2024

• Update Conda environment and Dockerfile

  fasterius

  committed
  12ca883

• Add QUARTONOTEBOOK nf-core module

  fasterius

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  3ced22c

• Use QUARTONOTEBOOK module in pipeline

  fasterius

  committed
  2e595b7

• Remove old local modules

  fasterius

  committed
  508c0b2

• Update changelog

  fasterius

  committed
  393bc3c

• Remove XDG paths, which are now in QUARTONOTEBOOK

  fasterius

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  64d3327

• Lower test thresholds

  fasterius

  committed
  fe7a7dc

• Revert "Lower test thresholds"

  Show description for 548bc67
  fasterius

  committed
  548bc67

• Fix report module output names and paths

  fasterius

  committed
  66e32bc

• Update Conda environment

  fasterius

  committed
  5226398

Commits on Feb 20, 2024

• Template update for nf-core/tools version 2.13

  nf-core-bot

  committed
  cd7a352

Commits on Feb 29, 2024

• Template update for nf-core/tools version 2.13.1

  nf-core-bot

  committed
  e9d1089

Commits on Mar 1, 2024

• Remove redundant environment specification

  fasterius

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  91ca58b

• Update MultiQC module

  fasterius

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  9539d6e

• Use Space Ranger output for MultiQC

  fasterius

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  1a42abf

• Add missing MultiQC output documentation

  fasterius

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  a095713

• Update changelog

  fasterius

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  f8c2863

Commits on Mar 4, 2024

• Fix tables writing in SpatialData objects

  cavenel

  committed
  01eefcc

• Fix quarto formatting

  cavenel

  committed
  d1bf3ec

• Move from SpatialDE to Squidpy for SVG computation

  cavenel

  committed
  c606f17

Commits on Mar 5, 2024

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

  fasterius

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  72f50c9

• Add util-subworkflows and move most lib/ content

  fasterius

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  52e4c21

• Merge branch 'TEMPLATE' into template-updates

  fasterius

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  eb23d32

• Add missing versions export for INPUT_CHECK

  fasterius

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  99d9a8f

• Add missing FastQC input to MultiQC

  fasterius

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  45de379

• Update UNTAR module

  fasterius

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  9b8e7d5

• Merge branch 'multiqc-spaceranger' into use-spatialdata

  fasterius

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  3901517

• Merge branch 'template-updates' into use-spatialdata

  fasterius

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  a35cd3b

• Update nf-test with new downstream subworkflow

  fasterius

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  c08398d

Commits on Mar 6, 2024

• Merge branch 'quartonotebook' into use-spatialdata

  fasterius

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  af53d94

• Add missing Spaceranger MultiQC input

  fasterius

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  370004d

• Fix notebook name and zarr/h5ad output patterns

  fasterius

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  0600a1e

Commits on Mar 7, 2024

• Fix SVG report test assertions

  fasterius

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  d8067c6

• Delete old spatial DE report

  fasterius

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  bef1ce5

• Fix publishing of AnnData object

  fasterius

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  c49f880

• Fix publishing of DEG CSV

  fasterius

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  3245e17

• Add testing of SpatialData output

  fasterius

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  d5f16b4

• Minor formatting

  fasterius

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  fcd5404

• Update snapshots

  fasterius

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  496a96e

Commits on Mar 19, 2024

• Rename SVG to spatially variable genes

  fasterius

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  9e907df

• Remove st_ prefix from names/variables/etc.

  fasterius

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  8238a32

• Update snapshots

  fasterius

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  4143983

Commits on Mar 20, 2024

• Update citations

  fasterius

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  354f3af

• Fix duplicate citation entries

  fasterius

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  2a9fb02

Commits on Mar 21, 2024

• Add pipeline logo to Quarto report ToCs

  fasterius

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  c0c19ad

Commits on Apr 2, 2024

• Downgrade Quarto to 1.3 due to figure formatting

  Show description for b275bc7
  fasterius

  committed
  b275bc7

• Update snapshots

  fasterius

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  d994410

• Include SpatialData description in all outputs

  cavenel

  committed
  5e64cd2

• Clean Spatially Variable Genes quarto markdown

  cavenel

  committed
  668d712

Commits on Apr 4, 2024

• Update changelog

  fasterius

  committed
  e103fc4

• Remove duplicate citation for SpatialData

  fasterius

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  4f12ac8

• Minor formatting

  fasterius

  committed
  f82267d

• Update quartonotebook module

  fasterius

  committed
  8ae8c26

• Update spaceranger/count module

  fasterius

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  d4861bd

• Remove TODO

  fasterius

  committed
  f253f56

Commits on Apr 12, 2024

• Update SpatialData to v0.1.2

  cavenel

  committed
  51d5918

• Remove temporary fix for scanpy issue

  cavenel

  committed
  a9a5570

• Add back missing line in SVG quarto

  cavenel

  committed
  b139755

• Fix spelling of AnnData

  cavenel

  committed
  d2a490b

• Clean read_zarr local path

  cavenel

  committed
  184dec8

• Fix qmd headers

  cavenel

  committed
  c364e3e

• Move degs/ output to data/ folder

  fasterius

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  6754c6f

• Add fix for pip install in Dockerfile

  fasterius

  committed
  72e07a0

• Fix adata import order

  cavenel

  committed
  de3c8c1

• Merge branch 'use-spatialdata' of https://github.com/nf-core/spatialtranscriptomics into use-spatialdata

  cavenel

  committed
  e6f156e

• Remove trailing whitespace

  cavenel

  committed
  a465e0f

• Export spatialdata_io version

  fasterius

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  7e1756f

• Remove Conda profile for READ_DATA process

  fasterius

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  7ec707c

• Update snapshots

  fasterius

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  509f547