nf-core / nf-core/seqinspector
Enable Element Bases2Fastq runfolder input to MultiQC
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enhancement
- Dominant language
- Nextflow
- Stars
- 28
- Forks
- 44
- Avg merge
- 11d 8h
- Merged PRs (30d)
- 2
Description
Description of feature
MultiQC can already parse the runfolder for Element Bioscience Bases2Fastq tools so we should take advantage of this within seqinspector, see https://docs.seqera.io/multiqc/modules/bases2fastq.
Relevant run-level metrics include:
- Polony counts and yields
- Base quality distributions (histogram and by-cycle)
- Index assignment statistics
- Per-sample sequence content and GC distribution
- Adapter content analysis
- Unassigned/unknown barcode sequences (run-level only)
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 inspecting how seqinspector currently passes runfolder inputs to MultiQC, then compare that flow with the MultiQC Bases2Fastq module documentation linked in the issue. The work is done when a Bases2Fastq runfolder is accepted and the generated MultiQC report includes the listed run-level and per-sample metrics.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 62/100