nf-core / nf-core/denovotranscript
Separate assemblies for separate samples
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- Dominant language
- Nextflow
- Stars
- 26
- Forks
- 3
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
Transferring Slack request to Github:
Currently the pipeline pools reads from all files in the samplesheet before proceeding with assembly. However, some users would find it useful to keep different samples separated and be able to generate multiple transcriptomes with only one run of the pipeline.
"I would absolutely love the pipeline to be upgraded to treat sample sheet entries with different sample names as different entries that should be kept separately, just as other nf-core pipelines such as Sarek and Rnaseq does."
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
The issue names no files, tests, or entry points. Start by tracing how samplesheet entries are grouped before assembly, then determine how separate sample names should produce independent transcriptomes in one run; done means pooled reads are no longer mixed across sample names and the resulting assemblies remain separate.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100