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