A uniform input for all tools in each screening workflow
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 119
- Forks
- 40
- Avg merge
- 2d 17h
- Merged PRs (30d)
- 5
Description
Description of feature
Currently different analysis software in ARG screening workflow use different input sequences.
For instance, AMRFinderPlus and RGI use nucleotide sequence as input whereas deeparg uses predicted protein sequences from the annotation step in the beginning of the pipeline.
Since all software accept both nucleotide and protein sequences, it would be really helpful to have a uniform input for all software which allows post-processing and comparison between predictions by different software based on sequence accession number.
https://nfcore.slack.com/archives/C02K5GX2W93/p1717515107461539
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 tracing the ARG screening workflow inputs for AMRFinderPlus, RGI, and deeparg, including the annotation step that supplies predicted proteins. Determine where the workflow selects nucleotide versus protein sequences and define acceptance checks showing that every tool uses one uniform input and produces outputs comparable by sequence accession number.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100