perf: cluster_config

defaults

@@ -30,6 +30,7 @@
   "sequenza_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sequenza:3.0.0",
   "msisensor_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/msisensor-pro:1.2.0",
   "tmb_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/tmb:1.0.0",
-  "cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "cluster_16cpu_32gb": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "cluster_2cpu_4gb": "OnDemand bcs.es.c.large img-ubuntu-vpc",
   "disk_size": "200"
 }

inputs

@@ -33,5 +33,6 @@
   "{{ project_name }}.baseline": "{{ baseline }}",
   "{{ project_name }}.ref_flat": "{{ ref_flat }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
-  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+  "{{ project_name }}.cluster_2cpu_4gb": "{{ cluster_2cpu_4gb }}",
+  "{{ project_name }}.cluster_16cpu_32gb": "{{ cluster_16cpu_32gb }}"
 }

workflow.wdl

@@ -54,7 +54,8 @@ workflow {{ project_name }} {
   Int? interval_padding
   
   String disk_size
-  String cluster_config
+  String cluster_2cpu_4gb
+  String cluster_16cpu_32gb
   
   if (tumor_fastq_1!= "") {
     call mapping.mapping as tumor_mapping {
@@ -71,7 +72,7 @@ workflow {{ project_name }} {
       ref_dir=ref_dir,
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call Metrics.Metrics as tumor_Metrics {
@@ -84,7 +85,7 @@ workflow {{ project_name }} {
       sample=sample_id + '.T',
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call Dedup.Dedup as tumor_Dedup {
@@ -95,7 +96,7 @@ workflow {{ project_name }} {
       sample=sample_id + '.T',
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call deduped_Metrics.deduped_Metrics as tumor_deduped_Metrics {
@@ -108,7 +109,7 @@ workflow {{ project_name }} {
       sample=sample_id + '.T',
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call BQSR.BQSR as tumor_BQSR {
@@ -125,7 +126,7 @@ workflow {{ project_name }} {
       sample=sample_id + '.T',
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
   }
   
@@ -144,7 +145,7 @@ workflow {{ project_name }} {
       ref_dir=ref_dir,
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call Metrics.Metrics as normal_Metrics {
@@ -158,7 +159,7 @@ workflow {{ project_name }} {
       regions=regions,
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call Dedup.Dedup as normal_Dedup {
@@ -169,7 +170,7 @@ workflow {{ project_name }} {
       sample=sample_id + '.N',
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
@@ -183,7 +184,7 @@ workflow {{ project_name }} {
       regions=regions,
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call BQSR.BQSR as normal_BQSR {
@@ -200,7 +201,7 @@ workflow {{ project_name }} {
       sample=sample_id + '.N',
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call Haplotyper.Haplotyper as Haplotyper {
@@ -216,7 +217,7 @@ workflow {{ project_name }} {
       regions=regions,
       docker=sentieon_docker,
       disk_size=disk_size,
-      cluster_config=cluster_config
+      cluster_config=cluster_16cpu_32gb
     }
 
     call bcftools.bcftools as Haplotyper_bcftools {
@@ -225,7 +226,7 @@ workflow {{ project_name }} {
       fasta=fasta,
       ref_dir=ref_dir,
       docker=bcftools_docker,
-      cluster_config=cluster_config,
+      cluster_config=cluster_2cpu_4gb,
       disk_size=disk_size
     }
   }
@@ -241,7 +242,7 @@ workflow {{ project_name }} {
     tumor_bam=tumor_BQSR.recaled_bam,
     tumor_bam_index=tumor_BQSR.recaled_bam_index,
     docker=manta_docker,
-    cluster_config=cluster_config,
+    cluster_config=cluster_16cpu_32gb,
     disk_size=disk_size
   }
   
@@ -252,7 +253,7 @@ workflow {{ project_name }} {
     germline_vcf=Manta.germline_vcf,
     annotsv_database=annotsv_database,
     docker=annotsv_docker,
-    cluster_config=cluster_config,
+    cluster_config=cluster_2cpu_4gb,
     disk_size=disk_size
   }
   
@@ -273,7 +274,7 @@ workflow {{ project_name }} {
     germline_resource=germline_resource,
     germline_resource_tbi=germline_resource_tbi,
     docker=sentieon_docker,
-    cluster_config=cluster_config,
+    cluster_config=cluster_16cpu_32gb,
     disk_size=disk_size
   }
   
@@ -283,7 +284,7 @@ workflow {{ project_name }} {
     fasta=fasta,
     ref_dir=ref_dir,
     docker=bcftools_docker,
-    cluster_config=cluster_config,
+    cluster_config=cluster_2cpu_4gb,
     disk_size=disk_size
   }
   
@@ -292,7 +293,7 @@ workflow {{ project_name }} {
     vcf=TNseq_bcftools.norm_vcf,
     annovar_database=annovar_database,
     docker=annovar_docker,
-    cluster_config=cluster_config,
+    cluster_config=cluster_16cpu_32gb,
     disk_size=disk_size
   }
   
@@ -307,7 +308,7 @@ workflow {{ project_name }} {
     tumor_bam_index=tumor_BQSR.recaled_bam_index,
     baseline=baseline,
     docker=msisensor_docker,
-    cluster_config=cluster_config,
+    cluster_config=cluster_2cpu_4gb,
     disk_size=disk_size
   }
   
@@ -322,7 +323,7 @@ workflow {{ project_name }} {
     tumor_bam=tumor_BQSR.recaled_bam,
     tumor_bam_index=tumor_BQSR.recaled_bam_index,
     docker=sequenza_docker,
-    cluster_config=cluster_config,
+    cluster_config=cluster_16cpu_32gb,
     disk_size=disk_size
   }
   
@@ -332,7 +333,7 @@ workflow {{ project_name }} {
     regions=regions,
     snpindel_txt=TNseq_ANNOVAR.multianno_txt,
     docker=tmb_docker,
-    cluster_config=cluster_config,
+    cluster_config=cluster_2cpu_4gb,
     disk_size=disk_size
   }
   
@@ -349,7 +350,7 @@ workflow {{ project_name }} {
     tumor_bam_index=tumor_BQSR.recaled_bam_index,
     hrd=HRD.hrd,
     docker=cnvkit_docker,
-    cluster_config=cluster_config,
+    cluster_config=cluster_2cpu_4gb,
     disk_size=disk_size
   }
 }