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feat(slurm-script): add reads support for combine #75

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Merged
rrwick merged 1 commit into from
Aug 31, 2026
Merged

feat(slurm-script): add reads support for combine #75

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6 changes: 4 additions & 2 deletions pipelines/Slurm_Autocycler_Bash_script_by_Michael_Hall/autocycler_slurm.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -408,7 +408,7 @@ if [[ "$keep_intermediate" = false ]]; then
fi

echo "[INFO] Running Autocycler compression, clustering, and resolution..."
autocycler compress -i assemblies -a autocycler_out 2>>autocycler.stderr
autocycler compress -i assemblies -a autocycler_out -t $threads 2>>autocycler.stderr
autocycler cluster -a autocycler_out 2>>autocycler.stderr

shopt -s nullglob
Expand All @@ -417,7 +417,7 @@ shopt -u nullglob

if ((${#clusters[@]} > 0)); then
for c in "${clusters[@]}"; do
autocycler trim -c "$c" 2>>autocycler.stderr
autocycler trim -c "$c" -t $threads 2>>autocycler.stderr
autocycler resolve -c "$c" 2>>autocycler.stderr
done

Expand All @@ -430,6 +430,8 @@ if ((${#clusters[@]} > 0)); then
autocycler combine \
-a autocycler_out \
-i "${final_gfas[@]}" \
-r "$reads" \
-t $threads \
2>>autocycler.stderr
else
echo "[WARN] No clusters found in autocycler_out/clustering/qc_pass/. Skipping resolution and combine steps."
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