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Description
Description
The output of the snippy subworkflow differs from documentation
Steps to Reproduce
Steps to reproduce the behavior:
bactopia --samples data/samplesheet.tsv --coverage 500 --max_cpus 16
bactopia --wf snippy --bactopia bactopia/ --reference genomic.gbff
Expected Behavior
Current output:
snippy-20250410-094938
├── core-snp-clean.full.aln.gz
├── core-snp.distance.tsv <================================ SNPDist?
├── core-snp.full.aln.gz
├── genomic.samples.txt
├── nf-reports
...
├── snippy-core
│ ├── core-snp.aln.gz
│ ├── core-snp.tab.gz
│ ├── core-snp.txt
│ ├── core-snp.vcf.gz
│ └── logs
...
├── snpdists
│ └── logs
EMPTY <====================================== EMPTY
└── software-versions
...
Docs has different output:
https://bactopia.github.io/latest/bactopia-tools/snippy/#output-overview
....
└── snpdists
├── core-snp.distance.tsv <==== this file is missing from output
└── logs
├── nf-snpdists.{begin,err,log,out,run,sh,trace}
└── versions.yml
Execution Environment
- Bactopia Version: bactopia 3.2.0
- OS: Ubuntu 22.04.5 LTS
- Environment: mamba 1.4.2 conda 23.3.1