vib-singlecell-nf/vsn-pipelines: v0.23.0

Implement the scATAC-seq preprocessing workflow (#245):

• Barcode correction [singlecelltoolkit, #249]
• "Debarcode" fastq files:
  • 10x [single_cell_toolkit, #249]
  • BioRad [BAP, #246]
• Adapter Trimming [Trim Galore / Cutadapt, #242]
• Mapping [bwa mem, #243]
  • mark duplicates [samtools markdup, #243]
• Generate fragments file [Sinto, #244]

Other scATAC-seq notes:

• Currently compatible with 10x-format fastq files (R1, R2[barcode reads], R3), and BioRad (R1, R2), which are processed with BAP.
• Added documentation for preprocessing steps
• The scATAC-seq workflows are in main_atac.nf and need to be referenced with the full path: vib-singlecell-nf/vsn-pipelines/main_atac.nf when running the pipeline.
• Added two additional input data types to getDataChannel: bam and fragments, both of which are loaded with their associated index file.

• celeda
  • Add ability to remove empty cells after applying DecontX
  • Fix plotting bug when no outliers are found
  • Add cell_annotate config entry
• scanpy
  • Add clustering preflight checks (vib-singlecell-nf/scanpy/issues/48)
  • Fixes to limit cpu usage in various processes.
  • Adaptive threshold cell filtering threshold (vib-singlecell-nf/scanpy/issues/47)
  • Add qc plots for n_counts filter in report notebook
  • Add single_sample_qc workflow
  • Bug fixes for mnncorrect, clustering, pca inputs
• pcacv
  • Adapt *-n-pc and k parameters if violating requirement of data dimensionality
  • Handle cases where no optimal number of PCs are found (vib-singlecell-nf/pcacv/issues/15)
  • Fix arguments passed to run_pca_cv.R
  • Fix vib-singlecell-nf/pcacv/issues/14
• sratoolkit
  • Fix missing assignment operator in config