nf-core / nf-core/genomeannotator
Question about --spaln_taxon
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- Dominant language
- Nextflow
- Stars
- 44
- Forks
- 17
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Description
Description of feature
Hi, I'm trying to include protein sequences from many related species of worms for training protein-coding genes (I have no target protein sequence for target species), and after ran Nextflow (nf-core/genomeannotator) I got error message about --spaln_taxon.
Error
-[nf-core/genomeannotator] Pipeline completed with errors-
ERROR ~ A process input channel evaluates to null -- Invalid declaration `val spaln_taxon`
-- Check script '/user/.nextflow/assets/nf-core/genomeannotator/subworkflows/local/spaln_align_protein.nf' at line: 38 or see '.nextflow.log' file for more details
I am unsure how many --spaln_taxon models should be specified when protein sequences from multiple related species are used. Is it possible to provide more than one taxon?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading subworkflows/local/spaln_align_protein.nf at line 38 and the .nextflow.log output mentioned in the report. Reproduce the pipeline input that triggers the null spaln_taxon value, then establish whether multiple taxa are supported and what the completed behavior or documentation should show.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100