diff --git a/data/workflow/WDL/metaT/metat_assembly.wdl b/data/workflow/WDL/metaT/metat_assembly.wdl index 8ae654a2..d8465e6d 100755 --- a/data/workflow/WDL/metaT/metat_assembly.wdl +++ b/data/workflow/WDL/metaT/metat_assembly.wdl @@ -8,6 +8,7 @@ task megahit_assembly{ # parameter from https://www.nature.com/articles/s41597-019-0132-4 command <<< + set -euo pipefail megahit --12 ${rqc_clean_reads[0]} -t ${no_of_cpus} -o out/ --out-prefix mh --k-list 23,43,63,83,103,123 mkdir -p ${assem_out_fdr} cat out/mh.contigs.fa |sed 's/>.*_/>${assem_out_prefix}_/'|sed 's/ .*//' > ${assem_out_fdr}/${assem_out_prefix}.contigs.fa @@ -20,6 +21,7 @@ task megahit_assembly{ runtime { docker: DOCKER cpu: no_of_cpus + memory: "120 GiB" } output{