[BUG] [scenic] Regulons can be missing in multi-runs mode
dweemx opened this issue · 0 comments
dweemx commented
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:
- 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'
}
[...]
- Run using this entry point:
nextflow -C nextflow.config run vib-singlecell-nf/vsn-pipelines -entry scenic
- 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