euler setup

cbg-ethz · Feb 25, 2025 · 8f3e1be · 8f3e1be
1 parent 772a8a2
commit 8f3e1be
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Showing 6 changed files with 51 additions and 12 deletions.
diff --git a/scripts/submit_vp_transformer.sh b/scripts/submit_vp_transformer.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+sbatch \
+    --mail-type=END \
+    --ntasks=1 \
+    --cpus-per-task=8 \
+    --mem-per-cpu=8000 \
+    --time=6:00:00 \
+    -o /cluster/home/koehng/logs/sr2silo.out \
+    -e /cluster/home/koehng/logs/sr2silo.err \
+    ./run_vp_transformer.sh
diff --git a/workflows/README.md → workflow/README.md b/workflows/README.md → workflow/README.md
diff --git a/workflows/Snakefile → workflow/Snakefile b/workflows/Snakefile → workflow/Snakefile
diff --git a/workflow/config.yaml b/workflow/config.yaml
@@ -0,0 +1,30 @@
+BASE_SAMPLE_DIR: "/cluster/project/pangolin/gordon_samples/samples"
+SAMPLE_BATCH_IDS:
+  A1_05_2024_10_08: "20241024_2411515907"
+  A2_17_2024_10_13: "20241024_2411515907"
+  A3_16_2024_10_12: "20241024_2411515907"
+  B1_05_2024_10_11: "20241024_2411515907"
+  B2_25_2024_10_08: "20241024_2411515907"
+  B3_16_2024_10_14: "20241024_2411515907"
+  C1_05_2024_10_13: "20241024_2411515907"
+  C2_25_2024_10_11: "20241024_2411515907"
+  C3_18_2024_10_09: "20241024_2411515907"
+  D1_10_2024_10_08: "20241024_2411515907"
+  D2_25_2024_10_13: "20241024_2411515907"
+  D3_18_2024_10_12: "20241024_2411515907"
+  E1_10_2024_10_11: "20241024_2411515907"
+  E2_15_2024_10_08: "20241024_2411515907"
+  E3_18_2024_10_14: "20241024_2411515907"
+  F1_10_2024_10_13: "20241024_2411515907"
+  F2_15_2024_10_11: "20241024_2411515907"
+  F3_19_2024_10_09: "20241024_2411515907"
+  G1_17_2024_10_08: "20241024_2411515907"
+  G2_15_2024_10_14: "20241024_2411515907"
+  G3_19_2024_10_12: "20241024_2411515907"
+  H1_17_2024_10_11: "20241024_2411515907"
+  H2_16_2024_10_09: "20241024_2411515907"
+  H3_19_2024_10_14: "20241024_2411515907"   
+TIMELINE_FILE: "/cluster/project/pangolin/work-vp-test/variants/timeline.tsv"
+PRIMERS_FILE: "/cluster/project/pangolin/work-new-variants/references/primers.yaml"
+NUC_REFERENCE: "sars-cov-2"
+RESULTS_DIR: "/cluster/project/pangolin/gordon_samples/25022025_unpaired"
diff --git a/workflow/submit_workflow.sh b/workflow/submit_workflow.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+sbatch \
+    --mail-type=END \
+    --ntasks=1 \
+    --cpus-per-task=24 \
+    --mem-per-cpu=8000 \
+    --time=2:00:00 \
+    -o /cluster/home/koehng/logs/sr2silo.out \
+    -e /cluster/home/koehng/logs/sr2silo.err \
+    snakemake -c 24
diff --git a/workflows/config.yaml b/workflows/config.yaml