Commits · main · DCNL / Nanopore · GitLab

Sep 07, 2026
- Merge branch 'feat/chrm-rescue' into 'main' · 054e2e91
  João Henrique Chrusciel authored Sep 07, 2026
  View commits for tag pipeline/2026-09-07 pipeline/2026-09-07
  
  054e2e91
- refactor: strip prose comments from code; rationale lives in docs · 8af62006
  João Henrique Chrusciel authored Sep 07, 2026
  8af62006
- pipeline: add the mt variant scan arm behind enable_mt_variant_scan, default off · c6184097
  João Henrique Chrusciel authored Sep 07, 2026
  c6184097
Sep 06, 2026
- qc: add heteroplasmy scan, spectrum and per-molecule phasing tools · e9776c27
  João Henrique Chrusciel authored Sep 06, 2026
  e9776c27
- qc: add mt_deletion_scan first-pass mtDNA deletion scan · 6cfe0c9a
  João Henrique Chrusciel authored Sep 06, 2026
  6cfe0c9a
- docs: record what the clip filter removes on the mitochondrial side · b490eff1
  João Henrique Chrusciel authored Sep 06, 2026
  b490eff1
- modkit: make the pass-threshold policy a parameter; rescue the human blood project · a32efefa
  João Henrique Chrusciel authored Sep 06, 2026
  a32efefa
- pipeline: add RESCUE_MT process · 037abfed
  João Henrique Chrusciel authored Sep 06, 2026
  037abfed
- docs: record the NUMT failure mode and the rescue design · 1a1a4030
  João Henrique Chrusciel authored Sep 06, 2026
  1a1a4030
- params: add letizia_mouse and nicotine_hippo_mm10 projects · b9495f1d
  João Henrique Chrusciel authored Sep 06, 2026
  b9495f1d
- qc: add mt_coverage_profile tool · 19fa2826
  João Henrique Chrusciel authored Sep 06, 2026
  19fa2826
- modkit: sample 50000 reads for mt-scope thresholds · 72aec970
  João Henrique Chrusciel authored Sep 06, 2026
  72aec970
Jun 14, 2026
- feat(groups): binary control-vs-user grouping (drop trauma 3-way split) · f17684d4
  João Henrique Chrusciel authored Jun 14, 2026
  View commits for tag paper/mtdna-human-blood-2026 paper/mtdna-human-blood-2026
  
  f17684d4
- fix(modkit): drop --seed (it forced --sampling-frac on small mtDNA BAMs) · 277e8382
  João Henrique Chrusciel authored Jun 14, 2026
  277e8382
- refactor(step3): shared MT-only BAM + auto 10th-percentile filter (MT-restricted) · 2524a0ca
  João Henrique Chrusciel authored Jun 14, 2026
  2524a0ca
- refactor(heteroplasmy): parse mutserve .txt table instead of VCF (smoke-validated) · c60c1669
  João Henrique Chrusciel authored Jun 14, 2026
  c60c1669
- fix(heteroplasmy): address adversarial review findings · b431ad71
  João Henrique Chrusciel authored Jun 14, 2026
  b431ad71
- feat: add mtDNA heteroplasmy calling (mutserve2) as a gated step-3 sub-flow · 9db9ba4e
  João Henrique Chrusciel authored Jun 14, 2026
  9db9ba4e
Jun 07, 2026
- Merge branch 'feat/desk-modkit' into 'main' · ef0d4cbb
  João Henrique Chrusciel authored Jun 07, 2026
  ef0d4cbb
- up: removed pipeline comments and created docs/pipeline_notes.md for clear guidance · fb970559
  João Henrique Chrusciel authored Jun 07, 2026
  
  fb970559
- Merge branch 'feat/desk-modkit' into 'main' · 53c6eadc
  João Henrique Chrusciel authored Jun 07, 2026
  53c6eadc
- up: rewrite README with mtDNA analysis, added haplogroup mapping. · 95a97df2
  João Henrique Chrusciel authored Jun 07, 2026
  
  95a97df2
Jun 03, 2026
- feat: dorado 2.0.0 and modkit 0.6.3 + mtDNA updated analyses + new QC analyses · bf8edb7b
  João Henrique Chrusciel authored Jun 03, 2026
  bf8edb7b
- feat: dorado 2.0.0 + modkit 0.6.3, [email protected] mods 5mC_5hmC+6mA, scipy build fix · 68a49da5
  João Henrique Chrusciel authored May 30, 2026
  
  68a49da5
Mar 20, 2026
- up: nextflow.config with new threshold of mapped reads · 48c258af
  Vinícius Boeira Pavani authored Mar 20, 2026
  
  48c258af
Feb 02, 2026
- UP: fast5 to pod5 conversion; basecall workflow logic; container with new packages. · 164c0210
  João Henrique Chrusciel authored Feb 02, 2026
  
  164c0210
Jan 17, 2026
- fix: fixed and issue with BASECALLING and QC where reads were not properly counted and processed · 6fa10732
  João Henrique Chrusciel authored Jan 17, 2026
  6fa10732
Dec 22, 2025
- up: added chrM filtering to modkit, minor update to the container, fixed... · e6d0c00e
  João Henrique Chrusciel authored Dec 22, 2025
  e6d0c00e
Dec 20, 2025
- up: nextflow.config to consider local raw files instead of SeaDrive · 1d32bacb
  João Henrique Chrusciel authored Dec 20, 2025
  
  1d32bacb
Dec 16, 2025
- fix: fixed an error with filter_bam.nf which was breaking the pipeline · d5bd929d
  João Henrique Chrusciel authored Dec 16, 2025
  
  d5bd929d
- feat: added support for SeaDrive · e12de173
  João Henrique Chrusciel authored Dec 16, 2025
  
  e12de173
Dec 11, 2025
- feat: implementing SeaDrive compatibility to test a new feature · 3150573c
  João Henrique Chrusciel authored Dec 11, 2025
  
  3150573c
- feat: refactored basecalling, updated coverage merge, enhanced modkit, unified... · 60be8035
  João Henrique Chrusciel authored Dec 11, 2025
  60be8035
Dec 10, 2025
- UP: modkit to test new features · 54a5bf26
  João Henrique Chrusciel authored Dec 10, 2025
  
  54a5bf26
Sep 08, 2025
- up: jq version upgrade · e2061533
  Carlos Gomes authored Sep 08, 2025
  
  e2061533
Sep 02, 2025
- Merge branch 'rm-null-defs' into 'main' · c92f1596
  Carlos Gomes authored Sep 02, 2025
  c92f1596
- fix: basecall channel value · 75a39f0a
  Carlos Gomes authored Sep 02, 2025
  
  75a39f0a
- fix: remove empty lines · 40ea279a
  Carlos Gomes authored Sep 02, 2025
  
  40ea279a
Aug 10, 2025
- Add comment explaining basecall_arg · 20d8a4d9
  Nicolas Cendron authored Aug 10, 2025
  20d8a4d9
Aug 09, 2025
- Merge branch 'cont-soft' into 'main' · 62f4b239
  Carlos Gomes authored Aug 09, 2025
  62f4b239