From 88406e584e68ffb1bb5e29b18600bd5edf5672d2 Mon Sep 17 00:00:00 2001
From: Tom Kasper <tom@tk-ai.eu>
Date: Sat, 3 Oct 2026 15:25:09 +0100
Subject: [PATCH] Updated config and resource requirements

---
 workflow/config/main.yaml            | 2 +-
 workflow/rules/baseline_pipeline.smk | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflow/config/main.yaml b/workflow/config/main.yaml
index 2ea6138..2626871 100644
--- a/workflow/config/main.yaml
+++ b/workflow/config/main.yaml
@@ -15,7 +15,7 @@ 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 : 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
 torch_env : '../envs/torch_cpu.yaml'
diff --git a/workflow/rules/baseline_pipeline.smk b/workflow/rules/baseline_pipeline.smk
index 8157214..b7fbf61 100644
--- a/workflow/rules/baseline_pipeline.smk
+++ b/workflow/rules/baseline_pipeline.smk
@@ -37,7 +37,7 @@ def get_batch_range(wildcards):
 rule download_nomiss_pod5:
     output:
         '../data/raw_pod5/nomiss/PBK98658_853a956f_57f83f46_{batch}.pod5'
-    threads: 1
+    threads: 4
     wildcard_constraints:
         batch="\d+"
     shell:
@@ -48,7 +48,7 @@ rule download_nomiss_pod5:
 rule download_trap_pod5:
     output:
         '../data/raw_pod5/trap/ATCC_25922_202309_0.pod5'
-    threads: 1
+    threads: 4
     wildcard_constraints:
         batch='\d+'
     shell: