This is a nextflow workflow for remapping reads to sets of virus sequences. In our lab we use it to validate virus sequences identified by metagenomic sequencing. It could be used as a stand-alone pipeline or as a subworkflow.
active 2024-08-30 → 2026-07-15 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 685 days from 2024-08-30 to 2026-07-15. Pushes: 26 total, peak 8 in a day. Pull requests: 0 total, peak 0 in a day. Issues: 6 total, peak 3 in a day. Comments: 0 total, peak 0 in a day. Stars: 0 total, peak 0 in a day.
- Pushes
- Pull requests
- Issues
- Comments
- Stars
Stars, PRs, issues and forks are under-captured in the later part of this window. GH Archive progressively stopped capturing non-push events during 2026 — −95% or worse by the end of the window. Every series here except Pushes fades for that reason, so a decline above reflects the archive, not this repository. Pushes stay reliable throughout, so read them, and the contributor counts derived from them, as the real signal. Data health has the measurements.
Top contributors
Pushes, PRs, issues, reviews and comments — stars and forks excluded, so this is contribution rather than popularity
| Contributor | Contributions | Pushes | PRs | Comments |
|---|---|---|---|---|
| stenglein-lab | 32 | 26 | 0 | 0 |
Recent activity
Latest issues, pull requests and releases
- Issue#5stenglein-lab2026-02-03 18:10A nice enhancement would be for the pipeline to be able to create new consensus sequences from mapped reads
- Issue#5stenglein-lab2026-02-03 18:10A nice enhancement would be for the pipeline to be able to create new consensus sequences from mapped reads
- Issue#4stenglein-lab2026-01-28 16:27test sample sheet refers to directory locations that are not valid paths if running from github
- Releasestenglein-lab2025-10-24 23:08v1.0
- Issue#2stenglein-lab2024-09-04 18:18Pipeline does not work for paired-end input fastq
- Issue#2stenglein-lab2024-09-04 18:17Pipeline does not work for paired-end input fastq
- Issue#1stenglein-lab2024-09-04 00:21The pipeline does not check that sample IDs on sample sheet and sample IDs from fastq file names are concordant
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 0 stars here means stars gained during the window, not the repo's star count.