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Updated config and resource requirements

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Tom Kasper
2026-10-03 15:25:09 +01:00
parent 97d9ddb2c5
commit 88406e584e
2 changed files with 3 additions and 3 deletions
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workflow/config/main.yaml
+1 -1
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@@ -15,7 +15,7 @@ fast_min_q: 8 # empty string or 0 to disable
# squiqqle dataset # squiqqle dataset
pod5_dataset: "nomiss_96BC_P2I_SUP_2026" pod5_dataset: "nomiss_96BC_P2I_SUP_2026"
pod5_dataset_size : 293 pod5_dataset_size : 293
pod5_stride : 600 # Use 1 in x pod5 files from the ONT NO-MISS dataset to reduce dataset size / compute requirements pod5_stride : 12 # Use 1 in x pod5 files from the ONT NO-MISS dataset to reduce dataset size / compute requirements
# custom ML # custom ML
torch_env : '../envs/torch_cpu.yaml' torch_env : '../envs/torch_cpu.yaml'
workflow/rules/baseline_pipeline.smk
+2 -2
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@@ -37,7 +37,7 @@ def get_batch_range(wildcards):
rule download_nomiss_pod5: rule download_nomiss_pod5:
output: output:
'../data/raw_pod5/nomiss/PBK98658_853a956f_57f83f46_{batch}.pod5' '../data/raw_pod5/nomiss/PBK98658_853a956f_57f83f46_{batch}.pod5'
threads: 1 threads: 4
wildcard_constraints: wildcard_constraints:
batch="\d+" batch="\d+"
shell: shell:
@@ -48,7 +48,7 @@ rule download_nomiss_pod5:
rule download_trap_pod5: rule download_trap_pod5:
output: output:
'../data/raw_pod5/trap/ATCC_25922_202309_0.pod5' '../data/raw_pod5/trap/ATCC_25922_202309_0.pod5'
threads: 1 threads: 4
wildcard_constraints: wildcard_constraints:
batch='\d+' batch='\d+'
shell: shell: