v0.8.1

Summary of changes:

• Improved workflow dag in #101
• Added case studies in readme
• QC report updates and fixes to data summary and display (#87, #63, #37, #102)
• Species option added (#44)

v0.8.0

Summary of changes:

• h5ad accepted as input files (#49), added h5ad profile and h5ad_single_sample workflow
• Display sample name instead of sample id in report plots (#81)
• SRAweb update
• Broken symlink (#82)
• Documentation updates: streamlined main readme
• Fixes for DockerHub references in submodules
• Updated master repo naming

v0.7.0

Summary of changes:

• Update nextflow version from 19.10.0 to 19.12.0-edge
• Implement FBgn to gene symbol conversion #92
• Implement autodetection of optimal number of PC for PCA #73
• Add multiple docs #84 #85
• Update submodules to latest commits 6ec17c4 91d29c5

v0.6.0

Summary of changes:

• Implement multi-sample params feature #20 [#79]*.
• Reports include manifest and params information #40 [5966798, 69c7beb]*.
• SCope tree parameters used when making loom #67 [3e3dcd0]*.
• Implement h5 compression on final loom #69 [d765201, f2db28b, c85950d]*.
• 10x input data now defined under params.data.tenx [fe2c30f].
• Fix bug: differential gene expression is run on log-normalized data now (raw data was used previously) #74 [4f7d49f].
• Fix for #77 [6a6fe8a].
• Fix for #68 [ef02b43].

* Currently, these features are only implemented for the following pipelines: single_sample, single_sample_star, bbknn, sra_cellranger_bbknn.

v0.5.0

Summary of changes:

• Run pipeline from SRA ID #28
• Clean and update #56
• Fix confetti bug [798f641]
• [utils] Add documentation for cell-based annotation [a78cbda]
• [utils] Label cells with barcode plus sample ID by default [8f9edfd]
• [scenic] Only save regulons used in AUCell [62b5125]

v0.4.0

Summary of changes:

• Requires Nextflow 19.10.0
• Merge #47 + 2cefca1: Add automated testing for single_sample, single_sample_scenic, scenic and bbknn.
• Merge branch bbknn_workflow_reporting (f1bb4e6) : Implement BBKNN workflow reporting.
• Merge #58 (Implement #46):Implement filter based on cell metadata.
• Merge #57 (Implement #41): Implement annotation based on cell metadata.
• Allow multiple samples to be run with the SCENIC pipelines at once (d4d613f).
• Allow to qsub specific steps of SCENIC (4f92cf9).
• Add mnnCorrect batch effect correction method (ea10169, 1aaea42).
• Update container for multi-runs SCENIC from dweemx/sctx-pyscenic version 0.9.19-4 to 0.9.19-6.
• Organise configs within the tools folders.
• Minor refactoring on file names.
• Multiple bug fixes.

0.3.4

Summary of changes:

• Fix bug pipelines not resuming properly (fix for #39)
• Switch from getBaseName to get the sample ID to strategy where it's passed as part of a tuple (#36).
• Save all regulons in Loom files (filtering step is done in SCope).
• Make one logic to export results to loom file (see bin/export_to_loom.py).
• Regulon occurrences are now saved in $params.sc.scenic.scenicoutdir/multi_runs_regulons_[mtf|trk] (fix for #33).
• Upgrade of dweemx/pySCENIC on Dockerhub from 0.9.18-2 to 0.9.19-4 (mainly for using Loompy v3).
• Reduce memory footprint for multi-runs aggregation of features step.
• Fix bug encoding gene occurrences in the loom row attribute.
• Additional bug fixes.
• Clean and refactoring of processes.

0.3.1

Summary of changes:

• Fixes for adding SCENIC visualizations to the loom file
• Cleanup of Scanpy reporting processes
• Added a report for SCENIC when running single_sample_scenic

0.3.0

Summary of changes:

• Add Nemesh pipeline (Drop-seq)
  • Update star module for reuse within the pipeline
• Allow to set specific cluster options (pmem) in GRNboost step (SCENIC)
• Update Scanpy container to 0.4.0: fix issues with Scanpy container version 0.3.0 and add bioservices module
• Update pySCENIC container with loompy 3

0.2.2: Updates and fixes for SCENIC multiruns workflow

SCENIC multiruns fixes