Commits · 3c523e2d9aa400277b56dfdb789a716e2dc6fcc4 · CCD-public / Nanopore · GitLab

Jul 21, 2025
- Merge branch 'dev/optm-sam-modkit' into 'main' · 3c523e2d
  Carlos Gomes authored Jul 21, 2025
  3c523e2d
- fix: shorten pod5 threads param · ab9adbef
  Carlos Gomes authored Jul 21, 2025
  
  ab9adbef
- fix: isize init and usage · 15aabcb1
  Carlos Gomes authored Jul 21, 2025
  
  15aabcb1
- fix: samtools threads option · 396542e5
  Carlos Gomes authored Jul 21, 2025
  
  396542e5
Jul 15, 2025
- Merge branch 'dev/work' into 'main' · 4b18e4fd
  Carlos Gomes authored Jul 15, 2025
  4b18e4fd
- up: set cleanup to true in config · 1a7f3313
  Carlos Gomes authored Jul 15, 2025
  
  1a7f3313
Jul 14, 2025
- up: clean-up procedure · 7b87f64b
  Carlos Gomes authored Jul 14, 2025
  
  7b87f64b
- fix: typo toc · aad5864f
  Carlos Gomes authored Jul 14, 2025
  
  aad5864f
Jul 12, 2025
- Merge branch 'main' into 'dev/optm-sam-modkit' · 79b0497e
  Carlos Gomes authored Jul 12, 2025
  79b0497e
- Merge branch 'dev/profiles' into 'main' · 4ffe9a9e
  Carlos Gomes authored Jul 12, 2025
  4ffe9a9e
- fix: slurm example using profiles insead of params-file · 8014695c
  Carlos Gomes authored Jul 12, 2025
  
  8014695c
- Merge branch 'main' into dev/profiles · e95e974d
  Carlos Gomes authored Jul 12, 2025
  
  e95e974d
- Merge branch 'main' into 'dev/optm-sam-modkit' · 633455f6
  Carlos Gomes authored Jul 12, 2025
  633455f6
- Merge branch 'dev/modkit-zip' into 'main' · e66c0d96
  Carlos Gomes authored Jul 12, 2025
  e66c0d96
- Merge branch 'dev/slurm-doc' into 'main' · 79eac2c3
  Carlos Gomes authored Jul 12, 2025
  79eac2c3
Jul 11, 2025
- up: add new optim parameters to the docs · 0fae03c1
  Carlos Gomes authored Jul 11, 2025
  
  0fae03c1
- up: samtools_threads is always used · 7b56be02
  Carlos Gomes authored Jul 11, 2025
  
  7b56be02
- up: support modkit optimization params in modkit step · 4b9e639c
  Carlos Gomes authored Jul 11, 2025
  
  4b9e639c
- up: support samtools threads in qc and modkit steps · ea570524
  Carlos Gomes authored Jul 11, 2025
  
  ea570524
- up: support samtools and fast5pod5 threads params in basecalling · 5d8f4252
  Carlos Gomes authored Jul 11, 2025
  
  5d8f4252
- up: params-file usage · 932e65f8
  Carlos Gomes authored Jul 11, 2025
  
  932e65f8
- up: mv human blood parameters to yaml files · 4c3fd222
  Carlos Gomes authored Jul 11, 2025
  
  4c3fd222
Jul 10, 2025
- up: add slurm script example to doc · 4ad3cfc4
  Carlos Gomes authored Jul 10, 2025
  
  4ad3cfc4
- up: modkit extract full using compression · 705f9048
  Carlos Gomes authored Jul 10, 2025
  
  705f9048
Jul 04, 2025
- Merge branch 'dev/docs' into 'main' · 308b23b4
  Carlos Gomes authored Jul 04, 2025
  308b23b4
Jun 30, 2025
- up: doc support for profile usage · 9ba483c7
  Carlos Gomes authored Jun 30, 2025
  9ba483c7
- up: put profiles in configs/ · aa2f168b
  Carlos Gomes authored Jun 30, 2025
  
  aa2f168b
- Merge branch 'dev/nxtcfg' into 'main' · 83fb6f59
  Carlos Gomes authored Jun 30, 2025
  83fb6f59
- fix: docs and nextflow main config · 9d836bda
  Carlos Gomes authored Jun 30, 2025
  9d836bda
- up: gpu comments + profiles usage · f8ce0a31
  Carlos Gomes authored Jun 30, 2025
  
  f8ce0a31
Jun 27, 2025
- up: README.md apptainer build and src folder. · 8fd54d80
  Mau Magnaguagno authored Jun 27, 2025
  
  8fd54d80
- up: nextflow.config with modkit profile · 57c707e2
  João Henrique Chrusciel authored Jun 27, 2025
  
  57c707e2
Jun 24, 2025
- up: basecalling, nextflow.config, nextflow parameters and readability · c64fa5de
  João Henrique Chrusciel authored Jun 24, 2025
  c64fa5de
Jun 20, 2025
- Merge branch 'dev/pipeline-mods' into 'main' · 17f1978e
  Carlos Gomes authored Jun 20, 2025
  17f1978e
- up: README.md and basecall.nf · bd18ebaa
  João Henrique Chrusciel authored Jun 20, 2025
  bd18ebaa
Jun 08, 2025
- fixed GPU access issue by adding --nvccli · 7498e42e
  João Henrique Chrusciel authored Jun 08, 2025
  
  7498e42e
Jun 07, 2025
- updated dorado to v1.0.1 · 6fad5285
  João Henrique Chrusciel authored Jun 07, 2025
  
  6fad5285
- fixed conventions in BASECALL and BASECALL_DEMUX processes · fea14747
  João Henrique Chrusciel authored Jun 07, 2025
  fea14747
May 27, 2025
- up: basecalling.nf code optmization · 82745392
  João Henrique Chrusciel authored May 27, 2025
  82745392
May 26, 2025
- Merge branch 'fix/strict-syntax' into 'main' · 38391d50
  Carlos Gomes authored May 26, 2025
  38391d50