adapt pbmm2 and pbindex resources to GREGoR data

Author: SHuang-Broad

wdl/pipelines/PacBio/Utility/ProcessOnInstrumentDemuxedChunk.wdl

@@ -121,7 +121,7 @@ workflow ProcessOnInstrumentDemuxedChunk {
     # prep work
 
     # where to store final results
-    String workflow_name = "ProcessOnInstrumentDemuxedChunk"
+    String workflow_name = "Realign"
     String outdir = sub(gcs_out_root_dir, "/$", "") + "/" + workflow_name
 
     # String bc_specific_out = outdir + '/' + readgroup_id

wdl/tasks/Utility/PBUtils.wdl

@@ -940,7 +940,6 @@ task Align {
 
     Boolean fix_library_entry = if defined(library) then true else false
 
-
     command <<<
     set -euxo pipefail
     start_time=$(date +%s)
@@ -992,16 +991,16 @@ task Align {
 
     #########################
 
-    Int disk_size = 1 + 3*ceil(size(bam, "GiB") + size(ref_fasta, "GiB"))
+    Int disk_size = 1 + 4*ceil(size(bam, "GiB") + size(ref_fasta, "GiB"))
     Int cpus = 16
-    Int mem = 24
+    Int mem = 64
 
     RuntimeAttr default_attr = object {
         cpu_cores:          cpus,
         mem_gb:             mem,
         disk_gb:            disk_size,
         boot_disk_gb:       10,
-        preemptible_tries:  2,
+        preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-smrttools:12.0.0.176214"
     }
@@ -1044,22 +1043,22 @@ task PBIndex {
 
     #########################
 
-    Int disk_size = 10 + ceil(size(bam, "GB"))
+    Int disk_size = 10 + ceil(size(bam, "GiB"))
 
     RuntimeAttr default_attr = object {
         cpu_cores:          2,
         mem_gb:             4,
         disk_gb:            disk_size,
         boot_disk_gb:       10,
         preemptible_tries:  1,
-        max_retries:        1,
+        max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-smrttools:12.0.0.176214"
     }
     RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
     runtime {
         cpu:                    select_first([runtime_attr.cpu_cores,         default_attr.cpu_cores])
         memory:                 select_first([runtime_attr.mem_gb,            default_attr.mem_gb]) + " GiB"
-        disks: "local-disk " +  select_first([runtime_attr.disk_gb,           default_attr.disk_gb]) + " SSD"
+        disks: "local-disk " +  select_first([runtime_attr.disk_gb,           default_attr.disk_gb]) + " HDD"
         bootDiskSizeGb:         select_first([runtime_attr.boot_disk_gb,      default_attr.boot_disk_gb])
         preemptible:            select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
         maxRetries:             select_first([runtime_attr.max_retries,       default_attr.max_retries])