add a marker line to tune

Author: SHuang-Broad

wdl/pipelines/ONT/Preprocessing/ONTFlowcellWGSuBAM.wdl

@@ -131,7 +131,7 @@ workflow ONTFlowcellWGSuBAM {
 
     ###################################################################################
     # prep work
-    String workflow_name = "ONTFlowcellWGSuBAM"
+    String workflow_name = "Realign"
     String outdir = sub(gcs_out_root_dir, "/$", "") + "/~{workflow_name}/~{flowcell}"
     String outdir_aln     = outdir + '/alignments'
     String outdir_metrics = outdir + '/metrics'

wdl/tasks/Alignment/AlignReads.wdl

@@ -50,6 +50,7 @@ task Minimap2 {
     Int desired_cpus = (if('LOCAL'==disk_type) then 32 else 24) * length(reads)
     Int cpus = if max_cpus < desired_cpus then max_cpus else desired_cpus  # WDL 1.0 doesn't have a max(,)....
     Int mem = cpus * (if('LOCAL'==disk_type || longer_ont_read_hint) then 6 else 5)
+    # if mimimap2 OoM, tune the line above
 
     Int mm2_threads = cpus - 2