Set homer cutoff

.gitignore

@@ -14,3 +14,8 @@ tmp/
 .java/
 .cache/
 .nv/
+
+# Beads / Dolt files (added by bd init)
+.dolt/
+*.db
+.beads-credential-key

rules/basic/analysis.smk

@@ -61,8 +61,8 @@ rule run_homer:
         outdir="output/homer/finemapped_results/{wildcards.experiment_label}"
         mkdir -p "$outdir"
 
-        # Skip HOMER gracefully if there are no finemapped windows.
-        if [ "$(zcat {input.finemapped_windows} | wc -l)" -eq 0 ]; then
+        # Skip HOMER gracefully if there are less than 5 windows (very minimal cutoff).
+        if [ "$(zcat {input.finemapped_windows} | wc -l)" -lt 5 ] || [ "$(zcat {input.background} | wc -l)" -lt 5 ]; then
             echo "No finemapped windows found. Skipping HOMER." | tee -a {log.stdout}
 
             cat > {output.report} <<EOF

rules/basic/repeat.smk

@@ -63,7 +63,7 @@ rule quantify_repeats:
     conda:
         "envs/bedbam_tools.yaml"
     resources:
-        mem_mb=lambda wildcards, attempt: 32000 * (1.5 ** (attempt - 1)),
+        mem_mb=lambda wildcards, attempt: 48000 * (2 ** (attempt - 1)),
         runtime=lambda wildcards, attempt: 60 * (2 ** (attempt - 1)),
     shell:
         r"""