diff --git a/metamorph b/metamorph index 2a6b4da..230b299 100755 --- a/metamorph +++ b/metamorph @@ -757,7 +757,6 @@ def parsed_arguments(name, description): def main(): - # Sanity check for usage if len(sys.argv) == 1: # Nothing was provided diff --git a/src/run.sh b/src/run.sh index cf3d4e8..b531542 100755 --- a/src/run.sh +++ b/src/run.sh @@ -103,7 +103,7 @@ function parser() { -t | --tmp-dir) provided "$key" "${2:-}"; Arguments["t"]="$2"; shift; shift;; -o | --outdir) provided "$key" "${2:-}"; Arguments["o"]="$2"; shift; shift;; -c | --cache) provided "$key" "${2:-}"; Arguments["c"]="$2"; shift; shift;; - -r | --triggers) provided "$key" "${2:-}"; Arguments["r"]="$2"; shift; shift;; + -r | --triggers) provided "$key" "${2:-}"; Arguments["r"]="${2/,/' '}"; shift; shift;; -* | --*) err "Error: Failed to parse unsupported argument: '${key}'."; usage && exit 1;; *) err "Error: Failed to parse unrecognized argument: '${key}'. Do any of your inputs have spaces?"; usage && exit 1;; esac @@ -199,9 +199,7 @@ function submit(){ # --printshellcmds --keep-going --rerun-incomplete # --keep-remote --restart-times 3 -j 500 --use-singularity # --singularity-args -B {}.format({bindpaths}) --local-cores 24 - triggers="${7:-'{code,params,software_env,input,mtime}'}" - if [[ ! ${triggers:0:1} == "{" ]] ; then triggers="{$triggers"; fi - if [[ ! ${triggers:0-1} == "}" ]] ; then triggers+='}'; fi + triggers="${7:-'code params software_env input mtime'}" rerun="--rerun-triggers $triggers" SLURM_DIR="$3/logfiles/slurmfiles"