v0.22.0

Summary of changes:

General changes

• Pre-filtering/pre-annotating (FILTER_AND_ANNOTATE_AND_CLEAN) is now performed outside of QC_FILTER 839735e a463b8a
• Add sanity check - Check if column containing sample ID exists in metadata file c32cfce
• *scrublet workflows - Publish data with doublets removed 47e611e
• Support to tag final output files (loom, h5ad) with the batch variabe for the harmony pipelines 822fc95
• Reformat popscle inputs Merge pull request #256 Closes #255
• Bug fix - Pipeline should output scopeloom instead of FINALIZE.out.scopeloom so that directs output will be included in final loom 22d587c
• Bug fix - Fix bug leading to out of sync issues of the input params of getChannel when calling it multiple times f50074a d0eb654
• Bug fix - Closes #260 2b1bd4e

Tools/Modules

• celda

  • Bug fix - Fix bug when plotting density plot when no outliers found 099b2f0
  • Add support to remove empty cells after DecontX matrix decontamination with the filterEmptyCells parameter 648b4df

• scanpy

  • Add plots for the n_counts filter in filter QC report python notebook and Closes vib-singlecell-nf/scanpy#47 b1923bb
  • Add single_sample_qc workflow 4915786
  • Set the n_jobs argument in regress out step using compute_resources__cpu label 23520e0
  • Disable BLAS multithreading in regress out step to reduce cpu usage (especially if n_jobs is > 1) 262c219
  • Add clustering preflight checks Closes vib-singlecell-nf/scanpy#48 debb6a1
  • Bug fix - Fix bug belong to scanpy not sc in config 26e57f2

• scenic

  • Bug fix - Use np.array_equel for array comparison instead of equality operator which won't work if array have different lengths d723bdd
  • Disable multi-threading for cisTarget and AUCell step to reduce cpu usage 2d9fa8f
  • Add TF-gene correlations to the SCENIC GRN output Merge pull request #257 Closes #254

• pcacv

  • Closes vib-singlecell-nf/pcacv#14 b543a8b
  • Closes vib-singlecell-nf/pcacv#8 ef7ab83
  • Closes vib-singlecell-nf/pcacv#15 b04d121
  • Adapt *-n-pc and k parameters if violating requirement of data dimensionality 228276f

• sratoolkit

  • Bug fix - Fix config: missing assignment operator 4d12b74

Docs

• Specify current Nextflow version to use in getting started docs Closes #250 923baad