v0.18.0

Summary of changes:

• Add support for Loom ; Closes #202
• Merge #201
• Switch back to HTTPS for submodules ; Closes #203
• Add support for hg19 38c117f vib-singlecell-nf/scenic@8c4fcc0
• Add support for mm10 (only motifs) eb918ca vib-singlecell-nf/scenic@ce98b89
• Allow min strategy for single_sample pipeline d394ac6
• Fixes vib-singlecell-nf/scanpy#43

v0.17.0

Summary of changes:

• Merge #199 : Implement #113
• Fix bug #197

v0.16.0

Summary of changes:

• Features
  • Merge #186 : Implement #180
  • Merge #190 : Implement #161
  • Add workflow to run Cell Ranger (w/ metadata file) + Sinlge-sample + SCENIC
• Docs
  • Update main README with pipeline table 3eff4b3 53bf138
  • Update docs for Cell Ranger input files 1fe7972
  • Update 2 and add 5 new case studies 80440a8
    • More detailed information at https://vsn-pipelines-examples.readthedocs.io/en/latest/
  • Other updates f8efa02
• Bug fixes
  • Fix #191
  • Fix #188
  • Other bug fixes 9d05e94 86274cd e315c42

v0.15.1

Summary of changes:

• Fix #181
• Fix vib-singlecell-nf/scenic#21
  • Any use of the APPEND_SCENIC_LOOM involving a loom from the pipeline and another loom not generated by the pipeline should be rerun

v0.15.0

Summary of changes:

• Add new popscle module (full free/demuxlet support) - Merge #173 : Implement #150
• Update docs and helper script for template/new submodules; 39ee333: Fix #144
• Restructuring docs: case studies moved to https://vsn-pipelines-examples.readthedocs.io/en/latest/
• Improve documentation 511709c 8daa014
• Fix #107
• Fix #169
• Fix #170
• Fix #171

v0.14.2

Summary of changes:

• Update version in manifest
• Update submodule references of pcacv, scanpy, scenic, sratoolkit

v0.14.1

Fixes:

• Fixed set seed to always be in params.global.seed (Fixes #165)
• Bugfix for single_sample loom file generation
• Fixes vib-singlecell-nf/scanpy#32 (report generation for parameter exploration mode)
• BBKNN workflow fix

Additions:

• Zenodo links

v0.14.0

Summary of changes:

• Add cellranger-atac workflow; Merge #89: Implement #134
• Allow to skip filtering and/or normalization step; Merge #163: Implement #149
  • Implemented for the following pipelines: single_sample, bbknn, harmony, mnncorrect pipelines
• Add support for Seurat Rds; Merge #162: implement #153
• Improve report notebooks for clustering, bbknn and mnncorrect #159 #160 (scanpy)
• Improve report notebooks for harmony #159 #160 (harmony)
• Fix #155
• Fix #158 (pcacv, harmony)
• Other changes 657e1bc vib-singlecell-nf/scenic@244830b

v0.13.4

Summary of changes:

• pySCENIC container update (v0.10.0):
  • Enables setting the seed in all steps
  • The GENIE3 is now available to use for the GRN inference step (the default is still GRNBoost2)
• Other container links updated

v0.13.3

Summary of changes:

• Use human readable identifier when parameter exploration on 78fb2e3 a7a7d08 vib-singlecell-nf/scanpy@b746f69
• Fix bug in report vib-singlecell-nf/scenic@266c17b vib-singlecell-nf/scenic#15
• Fix bug 5acc411 vib-singlecell-nf/scanpy@07663ab #135
• Fix bug param not used if exploration mode on vib-singlecell-nf/scanpy@b04397b