vib-singlecell-nf/vsn-pipelines

[BUG] [scenic] Regulons can be missing in multi-runs mode

dweemx opened this issue · 0 comments

Describe the bug
Motif- and track-based scenic was run twice. I get the track regulons, but not the motif regulons.

To Reproduce
Steps to reproduce the behavior:

  1. Configure with these options:
    Part of config which is causing the issue:
  [...]
   aucell {
      output = 'aucell_output.loom'
      rank_threshold = 5000
      auc_threshold = 0.05
      nes_threshold = 3.0
      min_genes_regulon = 5
      min_regulon_gene_occurrence = 5
   }
   numRuns = 2
   aggregate_features {
      use_chunking = true
      output_format = 'csv'
      compression = 'gzip'
   }
  [...]
  1. Run using this entry point:
nextflow -C nextflow.config run vib-singlecell-nf/vsn-pipelines -entry scenic
  1. See error:
    No errors. out/scenic/*/multi_runs_regulons_mtf was missing.

Expected behavior
Expecting to have results for regulons.

A sanity check should be performed in order to check that:

  • numRuns <= min_genes_regulon
  • numRuns <= min_regulon_gene_occurrence

Screenshots

Please complete the following information:

  • OS: CentOS7
  • Nextflow Version: 20.10.0
  • vsn-pipelines Version: 0.25.0

Additional context