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v0.20.0
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@cflerin cflerin released this 30 Sep 11:27
· 1836 commits to master since this release
v0.20.0
dcd7aac

Summary of changes

Major changes:

  • Add pcacv workflow to run PCACV 2741eb5
  • Specify compute resources using process labels. Merge #219 Closes #154
  • Remove the need of defining explicitly the helper functions (e.g.: parseConfig) inside the config dfa6af2 1ab9efb 5d74cb5
  • Implement feature to run pipelines on h5ad files with different suffixes (aka multi-labeled group strategy) 44d9aef de1f896
  • Allow user to run a workflow on a subset of cells from the data 83d6122 Closes #221
  • Don't include scope profile by default ad8115f
  • Publish pipeline final output only if params.utils.publish = true is in the config 33f643a

General changes:

  • Implement feature to beautify a h5ad file 1c41b42 6260b79

  • Add harmony workflow and related config 9c30059

  • Publish a loom with doublets info b46832f Closes #220

  • Add workflow cellranger_count_demuxlet to run Cell Ranger and Demuxlet at once 5240226

  • Add utility workflow to annotate data using a cell-based .tsv metadata file 39069dd

  • Add utility workflow to annotate and subsequently filter data using a cell-based .tsv metadata file

  • Add example config for SRA_TO_METADATA process 5adcbe9

  • Rename cellranger_metadata to cellranger_count_metadata 5abc06a

  • Abstract away code block used for cell filter, cell annotation and sample annotation into workflow ff1ab81

  • Add publish flag in cell_annotate and cell_filter 5bb233f

  • Allow to skip for a given sample the sample-based metadata annotation if not present in metadata 23e188c

  • Fixes bug where some columns from h5ad files were wrongly saved to either metric or annotation in loom 5711b35

  • Fixes #214

  • Other bug fixes:

  • Miscellaneous

  • Containers

    • Bump utils container version from 0.2.2 to 0.3.0 f262e88
    • Bump scrublet container version from 0.1.3 to 0.1.4 2ed2447
    • Bump scanpy container version from 0.5.0 to 0.5.2 2ed2447
    • Bump scenic container version from 0.10.0 to 0.10.3 8648758

Tools/Modules:

  • directs [NEW]
    • Merge #218 implements #216: module to automatically select default clustering
    • Allow the user to specify the cell embeddings (via cellEmbeddingsIndex param) to use for the density based clustering dfa1b27
  • scenic [UPDATE]
    • Allow to skip generating the reports e723e11
  • cellranger [UPDATE]
    • Allow n/a value in fastqs_dir_name column of metadata table 4866e82
    • With cellranger_count_metadata workflow, sample ID is defined as short_uuid + "__" + sample_name 4866e82
    • Allow the user to specify the chemistry parameter when running cellranger_count_metadata workflow 334137d
  • pcacv [UPDATE]
    • Set nCores to 1 in default config and "disable" multi-threading 9e52a96
    • Publish output files in data/pcacv folder as hard links 63428f1
    • Use dopar for parallelization 9b8d447
    • Increase max size of object to share with future package from 500Mb to 2Gb 8263f8c
  • scrublet [UPDATE]
    • Add sensible default values for Scrublet 57dd7d3

Docs:

  • Add docs for cellranger_count_metadata workflow 55626f0
  • Add docs regarding relevant output files generated by single_sample_scrublet pipeline cf73c3e a4e596d
  • Update docs related to cell-based metadata annotation feature 61ecbc7 a2c8e45
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