nf-core/spatialvi

Issues

• MultiQC 1.21 doesn't support genomic_dna section

  #84 opened 2 months ago by Alan-pad
  1

• Option to use the `--unknown-slide` parameter in `spaceranger count`

  #83 opened 2 months ago by pstorozenko
  1

• Aggregate samples into single object

  #56 opened a year ago by grst
  4

• Add MultiQC report

  #40 opened a year ago by grst
  12

• Create a workflow schematic

  #12 opened 6 months ago by fasterius
  1

• Rename the pipeline

  #65 opened 6 months ago by fasterius
  1

• Missing SpatialDE package in Docker container for ST_SPATIAL_DE process

  #74 opened 7 months ago by lealiaxiong
  3

• Add SpatialData as output

  #39 opened 7 months ago by grst
  20

• Use `to_legacy_anndata` function from `spatialdata_io` instead of custom code

  #75 opened 7 months ago by fasterius
  1

• Add checks for QC filtering

  #46 opened 10 months ago by fasterius
  2

• Add documentation for "Analysis options" in `usage.md`

  #32 opened a year ago by fasterius
  1

• Version exporting of `leidenalg` and `SpatialDE` does not work

  #51 opened a year ago by fasterius
  0

• Auto-detection of samplesheet type

  #47 opened a year ago by fasterius
  1

• Full-size test dataset

  #48 opened a year ago by grst
  0

• Implement tests using nf-test

  #36 opened a year ago by grst
  1

• Update spaceranger to 2.x

  #37 opened a year ago by grst
  8

• It should be possible to provide manual image alignments on a per-sample basis

  #38 opened a year ago by grst
  0

• Is Space Ranger Cytassist supported?

  #34 opened a year ago by pakiessling
  2

• Add documentation for all workflow parts

  #11 opened a year ago by fasterius
  0

• Create outputs readable by e.g. TissUUmaps, Loupe

  #14 opened a year ago by fasterius
  0

• Optimise input/output file formats

  #10 opened a year ago by fasterius
  0

• Add reporting of pipeline results

  #13 opened a year ago by fasterius
  1

• Harmonisation between Python / R

  #7 opened a year ago by fasterius
  0

• Remove redundant code

  #6 opened a year ago by fasterius
  1

• Add pre-processing subworkflow with SpaceRanger

  #9 opened 2 years ago by fasterius
  0

• Add Docker containers

  #8 opened 2 years ago by fasterius
  3

• Module compilation error - cause: unable to resolve class JsonSlurper

  #20 opened 2 years ago by vinsilico
  2

• Module compilation error

  #22 opened 2 years ago by mhjiang97
  2

• Add proper workflow/process inputs and outputs

  #5 opened 2 years ago by fasterius
  1