Summary of changes: Main 839735e a463b8a Pre-filtering/pre-annotating (FILTER_AND_ANNOTATE_AND_CLEAN) is now performed outside of QC_FILTER c32cfce Add sanity check - Check if column containing sample ID exists in metadata file 47e611e *scrublet workflows - Publish data with doublets removed 822fc95 Support to tag final output files (loom, h5ad) with the batch variabe for the harmony pipelines Merge pull request #256 - Reformat popscle inputs Closes #255 22d587c8 Bug fix - Pipeline should output scopeloom instead of FINALIZE.out.scopeloom so that directs output will be included in final loom. f50074a d0eb654 Bug fix - Fix bug leading to out of sync issues of the input params of getChannel when calling it multiple times 2b1bd4e Bug fix - Closes #260 Docs 923baad Specify current Nextflow version to use in getting started docs Closes #250 celda 099b2f0 Bug fix - Fix bug when plotting density plot when no outliers found. 648b4df Add support to remove empty cells after DecontX matrix decontamination with the filterEmptyCells parameter scanpy b1923bb Add plots for the n_counts filter in filter QC report python notebook and Closes vib-singlecell-nf/scanpy#47 4915786 Add single_sample_qc workflow 23520e0 Set the n_jobs argument in regress out step using compute_resources__cpu label 262c219 Disable BLAS multithreading in regress out step to reduce cpu usage (especially if n_jobs is > 1) debb6a1 Add clustering preflight checks Closes vib-singlecell-nf/scanpy#48 26e57f2 Bug fix - Fix bug belong to scanpy not sc in config scenic d723bdd Bug fix - Use np.array_equel for array comparison instead of equality operator which won't work if array have different lengths 2d9fa8f Disable multi-threading for cisTarget and AUCell step to reduce cpu usage Merge pull request #257 - Add TF-gene correlations to the SCENIC GRN output Closes #254 pcacv b543a8b Closes vib-singlecell-nf/pcacv#14 ef7ab834 Closes vib-singlecell-nf/pcacv#8 b04d121 Closes vib-singlecell-nf/pcacv#15 228276f Adapt *-n-pc and k parameters if violating requirement of data dimensionality sratoolkit 4d12b74 - Bug fix - Fix config: missing assignment operator