From 9b243278a1ae039cf2fbcd009417585e59a831d4 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 31 Aug 2026 10:27:49 +1000 Subject: [PATCH] Add reads support for combine --- .../autocycler_slurm.sh | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pipelines/Slurm_Autocycler_Bash_script_by_Michael_Hall/autocycler_slurm.sh b/pipelines/Slurm_Autocycler_Bash_script_by_Michael_Hall/autocycler_slurm.sh index ab3e273..5c999cb 100755 --- a/pipelines/Slurm_Autocycler_Bash_script_by_Michael_Hall/autocycler_slurm.sh +++ b/pipelines/Slurm_Autocycler_Bash_script_by_Michael_Hall/autocycler_slurm.sh @@ -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 $threads 2>>autocycler.stderr autocycler cluster -a autocycler_out 2>>autocycler.stderr shopt -s nullglob @@ -417,7 +417,7 @@ shopt -u nullglob if ((${#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 @@ -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."