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

workflow/envs/bam2parquet.yaml

@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python=3.14
+  - pysam=0.24
+  - pandas=3.0
+  - pyarrow
+  - biopython
+  - pydantic

workflow/envs/samtools.yaml

@@ -1,3 +1,4 @@
+name: samtools-test
 channels:
   - bioconda
 dependencies:

workflow/envs/torch_cpu.yaml

@@ -0,0 +1,17 @@
+name: e1-torch-cpu
+channels:
+  - conda-forge
+dependencies:
+  - python=3.14
+  - pytorch=2.13.*=cpu*
+  - numpy>=2.0,<3
+  - polars>=1.0
+  - pip
+  - pytest>=8
+  - pip:
+      - pod5
+        # E1 genus probe package, checked out as the `custom_models` submodule
+        # in the repo root (torch comes from conda here and satisfies the
+        # requirement, so only this package gets installed).
+        # Relative path assumes snakemake is invoked from `workflow/`.
+      - ../custom_models

workflow/envs/torch_cuda.yaml

@@ -0,0 +1,15 @@
+name: e1-torch-cuda
+channels:
+  - conda-forge
+dependencies:
+  - python=3.14
+  - pytorch=2.13.*=cuda129*
+  - numpy>=2.0,<3
+  - polars>=1.0
+  - pip
+  - pip:
+      - pod5
+        # E1 genus probe package, checked out as the `custom_models` submodule
+        # in the repo root (torch comes from conda here).
+        # Relative path assumes snakemake is invoked from `workflow/`.
+      - ../custom_models