A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).
active 2024-10-02 → 2026-07-07 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 644 days from 2024-10-02 to 2026-07-07. Pushes: 84 total, peak 7 in a day. Pull requests: 7 total, peak 3 in a day. Issues: 13 total, peak 1 in a day. Comments: 46 total, peak 4 in a day. Stars: 7 total, peak 1 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 |
|---|---|---|---|---|
| lbeltrame | 127 | 75 | 7 | 36 |
| SaraPotente | 10 | 8 | 0 | 0 |
| imdanique | 4 | 0 | 0 | 3 |
| ahwanpandey | 4 | 0 | 0 | 3 |
| aeeckhou | 2 | 0 | 0 | 1 |
| riederd | 2 | 0 | 0 | 1 |
| pblpez | 2 | 0 | 0 | 1 |
| Akazhiel | 1 | 0 | 0 | 0 |
| stephenturner | 1 | 0 | 0 | 0 |
| github-actions[bot] | 1 | 0 | 0 | 1 |
Recent activity
Latest issues, pull requests and releases
- Issue#62aeeckhou2026-01-26 09:43Questions regarding Panel Of Normal (PoN) for sWGS & SAMURAI analyzes
- Issue comment#62aeeckhou2026-01-26 09:43Questions regarding Panel Of Normal (PoN) for sWGS & SAMURAI analyzes
- Issue comment#62lbeltrame2026-01-19 11:02Questions regarding Panel Of Normal (PoN) for sWGS & SAMURAI analyzes
- Issue#61lbeltrame2025-12-15 13:43WisecondorX concatenate module does not add the sample name anymore
- Issue comment#59ahwanpandey2025-12-12 20:26Signature quantification step fails when running pipeline on just one sample
- Issue#59lbeltrame2025-12-12 07:45Signature quantification step fails when running pipeline on just one sample
- Issue comment#58lbeltrame2025-12-12 07:40FASTQC command number expected for "--memory"
- Issue#36lbeltrame2025-12-10 07:35Adjust bwa-mem parameters when dealing with cfDNA
- Issue comment#58ahwanpandey2025-12-09 23:08FASTQC command number expected for "--memory"
- Issue comment#57lbeltrame2025-12-09 09:04Update ichorCNA to the nf-core upstream versions
- Issue comment#58lbeltrame2025-12-09 09:03FASTQC command number expected for "--memory"
- Issue#58ahwanpandey2025-12-09 04:29FASTQC command number expected for "--memory"
- Pull request#57lbeltrame2025-11-18 14:11
- Releaselbeltrame2025-11-17 07:13v1.3.1 - "Mori Ranmaru"
- Releaselbeltrame2025-11-12 12:12v1.3.0 - "Uesugi Kenshin"
- Issue comment#21lbeltrame2025-11-11 09:31Refactor pipeline to properly access parameters
- Issue comment#55lbeltrame2025-11-07 12:32Refactor `params` usage in the pipeline
- Issue comment#56lbeltrame2025-11-06 10:37Paired Tumor/Normal workflow for ASCAT sc; sample concordance analyses for sWGS
- Issue comment#54ahwanpandey2025-11-06 10:14Add RGID tags to files produced by MarkDuplicates
- Issue comment#55github-actions[bot]2025-11-06 08:04Refactor `params` usage in the pipeline
- Issue comment#56lbeltrame2025-11-05 06:55Paired Tumor/Normal workflow for ASCAT sc; sample concordance analyses for sWGS
- Pull request#55lbeltrame2025-11-04 13:25
- Issue comment#54lbeltrame2025-11-03 13:16Add RGID tags to files produced by MarkDuplicates
- Issue comment#54lbeltrame2025-11-03 12:57Add RGID tags to files produced by MarkDuplicates
- Issue comment#51lbeltrame2025-10-30 13:11Use upstream nf-core module for WisecondorX
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 7 stars here means stars gained during the window, not the repo's star count.