Merge technical replicates (SRR1 + SRR2 -> SRX)
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 45/100
- Issue type
- Feature
- Clarity
- Mostly clear
- Activity status
- Stale
- Domain
- bioinformatics
Research direction
No source files or tests are named. Start by reading the linked fetchngs usage documentation and tracing how SRR/ERR/DRR identifiers resolve to SRX/ERX/DRX experiments. Done means technical replicate FASTQ files are concatenated per index within each experiment, including both R1 and R2 outputs.
Written by the indexing model from the issue text.
Description
Description of feature
The feature I'm hoping for is merging of technical replicates / runs (SRRs) within each sample/experiment (SRX/GSM/etc). I would like the fastq files to be concatenated within each index (SRR1.R1.fq + SRR2.R1.fq -> SRX.R1.fq; SRR1.R2.fq + SRR2.R2.fq -> SRX.R2.fq). Is such a feature possible in the current pipeline? This would be really nice for those who wish to go directly from fetchngs to other nf-core pipelines.
The docs suggest this should be possible (link), but it doesn't seem to be implemented yet.
- Dominant language
- Nextflow
- Stars
- 202
- Forks
- 96
- Avg merge
- 6h 36m
- Merged PRs (30d)
- 4
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