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nf-core/spatialvi: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[Unreleased]

Initial release of nf-core/spatialvi, created with the nf-core template. This marks the point at which the 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 reduction, clustering, differential expression testing as well as output files compatible with further downstream analyses and/or exploration in e.g. TissUUmaps or bespoke user code.

Added

  • Add quality control metrics as custom MultiQC content [#88]
  • Add MultiQC support for Space Ranger outputs [#70]
  • Use the QUARTONOTEBOOK nf-core module instead of local Quarto-based modules [#68]
  • Add support for SpatialData [$67]
  • Add a custom nf-core Quarto template for the downstream analysis reports [#64]
  • Allow input directories fastq_dir and spaceranger_dir to be specified as tar archives (.tar.gz)
  • Add a check to make sure that there are spots left after filtering [#46]
  • Implement tests with nf-test [#42]
  • Replace custom code to download reference with untar module [#44]
  • Embed resources in quarto reports [#43]
  • Use a samplesheet for input specification [#30, #31 and #45]
  • Add Space Ranger pre-processing as an optional pipeline step using the spaceranger nf-core module [#17 and #45]
  • Add env/ directory with pipeline-specific container and Conda environment specifications [#17 and #28]
  • Use a more standardised practice to find mitochondrial genes [#30]
  • Make pipeline output compatible with TissUUmaps [#31]
  • Add custom Quarto-based reports for all downstream processing [#31]
  • Embed resources in quarto reports [#43]

Fixed

  • #51: Fix version export of leidenalg and SpatialDE Python modules
  • #38: Specify manual alignment files in samplesheet
  • #20 and #22: Add missing Groovy module
  • #53: Use ensemble IDs as index in adata.var and fix related issue with SpatialDE

Dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool.

Dependency Version
SpatialDE 1.1.3
leidenalg 0.9.1
python 3.12.0
quarto 1.3.302
scanpy 1.9.3

Removed

  • Streamline pipeline for basic ST data processing; remove SC processing and deconvolution (for now) [#31]

v0.1.0 - 2023-03-31

Initial release of nf-core/spatialvi, created with the nf-core template by the Jackson Laboratory contributors (see README.md for details).