🧠 add CPU hooks for memory tasks

kids-first · Nov 5, 2024 · 0e35fb0 · 0e35fb0
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diff --git a/docs/KFDRC_SENTIEON_ALIGNMENT_GVCF_WORKFLOW_README.md b/docs/KFDRC_SENTIEON_ALIGNMENT_GVCF_WORKFLOW_README.md
@@ -90,6 +90,12 @@ Metrics collection and contamination estimation are unchanged.
 | Gather VCFs                | Picard MergeVcfs                    | No splitting occurs in Sentieon     |
 | Metrics                    | Picard CollectVariantCallingMetrics | Picard CollectVariantCallingMetrics |
 
+### Workflow Troubleshooting
+
+- Sentieon tools scale up RAM usage to match allocated CPUs. If a task that is
+  running into memory issues, that can be solved by EITHER scaling UP the
+  task's allocated RAM and scaling DOWN the tasks allocated CPUs.
+
 ## Basic Info
 - [D3b dockerfiles](https://github.com/d3b-center/bixtools)
 - Testing Tools:

diff --git a/workflows/kfdrc_sentieon_alignment_wf.cwl b/workflows/kfdrc_sentieon_alignment_wf.cwl
@@ -176,7 +176,9 @@ inputs:
   bamtofastq_ram: {type: 'int?', default: 2, doc: "RAM in GB to allocate to bamtofastq"}
   bwa_cpu: {type: 'int?', default: 36, doc: "CPUs to allocate to Sentieon BWA"}
   bwa_ram: {type: 'int?', default: 72, doc: "RAM in GB to allocate to Sentieon BWA"}
+  dedup_cpu: {type: 'int?', default: 32, doc: "CPUs to allocate to Sentieon DeDup"}
   dedup_ram: {type: 'int?', default: 32, doc: "RAM in GB to allocate to Sentieon DeDup"}
+  bam_to_cram_cpu: {type: 'int?', default: 16, doc:  "CPUs to allocate to Sentieon BAM to CRAM"}
   bam_to_cram_ram: {type: 'int?', default: 16, doc:  "RAM in GB to allocate to Sentieon BAM to CRAM"}
   run_t1k: {type: 'boolean?', default: true, doc: "Set to false to disable T1k HLA typing"}
   hla_dna_ref_seqs: {type: 'File?', doc: "FASTA file containing the HLA allele reference sequences for DNA.", "sbg:suggestedValue": {
@@ -345,6 +347,7 @@ steps:
       sentieon_license: sentieon_license
       reference: untar_reference/indexed_fasta
       in_alignments: sentieon_bwa_mem_payloads/realgn_bam
+      cpu_per_job: dedup_cpu
       mem_per_job: dedup_ram
     out: [metrics_file, out_alignments]
   sentieon_bqsr:
@@ -388,6 +391,7 @@ steps:
         valueFrom: $(self.nameroot).cram
       rm_cram_bai:
         valueFrom: $(1 == 1)
+      cpu_per_job: bam_to_cram_cpu
       mem_per_job: bam_to_cram_ram
     out: [output_reads]
   sentieon_hsmetrics: