v0.19.0

Summary of changes:

• Upgrade to Nextflow v20.04.1 Closes #182
• Fixes #210 #165
  • To have reproducible results with pipelines involving Harmony, this version of the pipelines is required.
• Improve annotation detection when convert h5ad to loom d599b9a
• Publish files to be staged through PUBLISH module eb4d6c4
  • Important intermediate files are published (hardlinked) in out/data:
    • e1821a5
    • vib-singlecell-nf/harmony@bfac8ff
    • vib-singlecell-nf/scanpy@86d1456
    • vib-singlecell-nf/scanpy@15eed53
    • vib-singlecell-nf/scanpy@5321fc5
  • They undergo additional compression ad15e59
    • Compression level can be set with params.utils.publish.compressionLevel
  • In exploration mode, some published (*final_output*) files have been reduced in size Closes #211
• Fix bug in cell tagging 9becc28 fdeeab1
• Closes vib-singlecell-nf/pcacv#11
• Fixes vib-singlecell-nf/pcacv#9
• Update vib-singlecell-nf/pcacv Dockerfile
  • Bump version from 0.1.0 to 0.2.0
• In bbknn, Run UMAP before cluster identification vib-singlecell-nf/scanpy@b5fbb64
• Fix bug where additional plots in report were empty vib-singlecell-nf/scanpy@98bff00
• Properly transfer the seed when running clustering vib-singlecell-nf/scanpy@44fc0b9 vib-singlecell-nf/scanpy@7220ed9
• Update Create module docs with latest code changes 02f75a3