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Added custom models as submodule, added pipleline for trap species handling (up to alignment). Initial progress on custom model rules

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This commit is contained in:
Tom Kasper
2026-10-03 15:16:36 +01:00
parent 3b93ceaf6e
commit f0cd594148
17 changed files with 270 additions and 21 deletions
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workflow/config/main.yaml
+8 -1
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@@ -1,5 +1,7 @@
tmp_dir: "/tmp"
seed : 0
# dorado
dorado_model_dir : "../dorado_models"
hac_model_name: "dna_r10.4.1_e8.2_400bps_hac@v6.0.0"
@@ -13,4 +15,9 @@ fast_min_q: 8 # empty string or 0 to disable
# squiqqle dataset
pod5_dataset: "nomiss_96BC_P2I_SUP_2026"
pod5_dataset_size : 293
pod5_stride : 12 # Use 1 in x pod5 files from the ONT NO-MISS dataset to reduce dataset size / compute requirements
pod5_stride : 600 # Use 1 in x pod5 files from the ONT NO-MISS dataset to reduce dataset size / compute requirements
# custom ML
torch_env : '../envs/torch_cpu.yaml'
budget_tolerance : 0.1
reads_per_genus : 5000