v0.13.2

Summary of changes:

• Fix bug FDRs missing in final loom 658eecf. This bug was inadvertently introduced in v0.13.0

v0.13.1

Summary of changes:

• Fix bug marker genes wrongly linked to clusters in final loom file 7bc4d11. This bug was inadvertently introduced in v0.13.0

v0.13.0

Summary of changes:

• Clean config parameters b6fe7bf d601947 1f9dcf0
• Rename data input parameters bc289fb 100efef
  • see Input Data Format docs
• Add regress out variable step 923a960 b3ac939
  • This step is not performed by default
  • see Regress Out Variables docs
• Explicitly subset highly variable genes vib-singlecell-nf/scanpy#20
• Use by default highly variable genes vib-singlecell-nf/pcacv@b457493
• Set clusterOptions to be process specific vib-singlecell-nf/scenic@bd3d1f5
• Add progress monitoring for grnboost2 w/o dask vib-singlecell-nf/scenic@bbdd25a
• Add case study Kurmangaliyev Y Z et al., 2019 40b092c
• Workflows are data input type agnostic #136 #110
• Workflows are fully reproducible #43
  • Except AUCell see vib-singlecell-nf/scenic#13
• Fix bug unpaired reports (clustering and batch effect correction) c851207 vib-singlecell-nf/scanpy@9b2684c
• Fix important bug in mnncorrect pipeline 07ce04c vib-singlecell-nf/scanpy#22
• Update DAGs 2af9ab5
• Add new CI for bbknn_scenic pipeline ad6d89f e365d45 468ad10 7b35333 27cb082

v0.12.1

Summary of changes:

• Fix bugs and improve report when parameter exploration mode is on vib-singlecell-nf/scenic@2339677
• Fix input cardinality issues for mnncorrect harmony pipelines vib-singlecell-nf/scanpy@01364c9
• Set maxForks to 2 for report generation processes vib-singlecell-nf/scanpy@01364c9

v0.12.0

Summary of changes:

• Implement SCENIC append only mode 48b8367 vib-singlecell-nf/scenic@4df02e2 vib-singlecell-nf/scenic@13acdc3
• Activate notification when submitting Cell Ranger count process to qsub system cellranger
• Use t-SNEs and UMAP plots in harmony report vib-singlecell-nf/harmony@914f9bd vib-singlecell-nf/harmony@0b7bd9e harmony
• Fix bug join channels on params leading to input file name collision vib-singlecell-nf/harmony@4acbf88 harmony vib-singlecell-nf/scanpy@0ad7d1f scanpy
• Fix bug Neighborhood graph should be recomputed after harmony vib-singlecell-nf/harmony@bd1b839 harmony
• Fix bug wrong container url in config vib-singlecell-nf/pcacv@a22d4ef pcacv
• Fix bugs in the neighbors graph process vib-singlecell-nf/scanpy@2bd5c12 vib-singlecell-nf/scanpy@7d37ed2 scanpy

v0.11.0

Summary of changes

• Use fixed seed (by default) for nondeterministic process #129 #43 f439771
• Run Cell Ranger using metadata file vib-singlecell-nf/scanpy#2 vib-singlecell-nf/scanpy#1 cab1b73
• Neighborhood graph computation has its own process
• Finalize mnncorrect pipeline 4d0b89a 97e3b8c
• Allow to start the single_sample pipeline with tsv or csv files
• Bug fix 07e3f73
• Update DAGs a297fc0
• Update docs 8190b49

v0.10.0

Summary of changes

• Enhance documentation
  • Create Read the Docs #124 #107
  • Add create module tutorial to RtD a75fbb6
• Add Harmony pipeline #125 #114
• Set log FC threshold to 0 for SCope loom c4e0b93
• Bug fixes ec2afe0 4292f3d af05f56

v0.9.1

Summary of changes:

• Improve parameter exploration strategy to handle empty params

v0.9.0

Summary of changes:

• Add parameter exploration for clustering step #115 #117
  • Currently only method and resolution parameter are implemented
• Add leiden algorithm in scanpy tool vib-singlecell-nf/scanpy#8 vib-singlecell-nf/scanpy#9

v0.8.2

Summary of changes:

• Default configuration files are now loaded before loading any profile-specific configs. This allows parameters in optional profiles to overwrite those set by the default profiles.
• Clarifications to the h5ad input profile, including setting of some default options.
• Changes to published loom files:
  • The compressed loom file is no longer published to out/loom/ since it's not compatible with SCope.
  • The filtered loom file (for input to SCENIC) is not longer published in out/loom
  • The "final" SCope-ready output loom is now named more descriptively: from ...SC__H5AD_TO_LOOM.loom, the output file is now named: {project_name}.{sampleId}.SCope_output.loom