add --save_merged_fastq for merging technical repeats to fetchngs
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enhancement
- Dominant language
- Nextflow
- Stars
- 202
- Forks
- 93
- Avg merge
- 1d 18m
- Merged PRs (30d)
- 15
Description
Description of feature
Hi nfcore/fetchngs team,
It would be awesome to add --save_merged_fastq for merging technical repeats to fetchngs. Would be very useful for downstream programs that cant deal with technical repeats.
Often easy to identify technical repeats from GEO because although technical repeats each have unique run_accession they share the same experiment_alias.
Many thanks,
Oliver
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 locating fetchngs's command-line option handling and workflow entry point, then trace how technical repeats are represented by shared experiment_alias values. Done means --save_merged_fastq merges those repeats and produces saved merged FASTQ files for downstream use.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, data-engineering
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100