test add bam

defaults

@@ -1,6 +1,12 @@
 {
   "tumor_fastq_1": "",
   "tumor_fastq_2": "",
+  "normal_fastq_1": "",
+  "normal_fastq_2": "",
+  "tumor_deduped_bam": "",
+  "tumor_deduped_bam_index": "",
+  "normal_deduped_bam": "",
+  "normal_deduped_bam_index": "",
   "fasta": "GRCh38.d1.vd1.fa",
   "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "dbsnp": "dbsnp_146.hg38.vcf",

inputs

@@ -4,6 +4,10 @@
   "{{ project_name }}.tumor_fastq_2": "{{ tumor_fastq_2 }}",
   "{{ project_name }}.normal_fastq_1": "{{ normal_fastq_1 }}",
   "{{ project_name }}.normal_fastq_2": "{{ normal_fastq_2 }}",
+  "{{ project_name }}.tumor_deduped_bam": "{{ tumor_deduped_bam }}",
+  "{{ project_name }}.tumor_deduped_bam_index": "{{ tumor_deduped_bam_index }}",
+  "{{ project_name }}.normal_deduped_bam": "{{ normal_deduped_bam }}",
+  "{{ project_name }}.normal_deduped_bam_index": "{{ normal_deduped_bam_index }}",
   "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
   "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
   "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",

workflow.wdl

@@ -18,8 +18,12 @@ workflow {{ project_name }} {
   String sample_id
   File? tumor_fastq_1
   File? tumor_fastq_2
-  File normal_fastq_1
-  File normal_fastq_2
+  File? normal_fastq_1
+  File? normal_fastq_2
+  File? tumor_deduped_bam
+  File? tumor_deduped_bam_index
+  File? normal_deduped_bam
+  File? normal_deduped_bam_index
 
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
@@ -137,80 +141,122 @@ workflow {{ project_name }} {
     }
   }
 
-  call mapping.mapping as normal_mapping {
-    input: 
-    group=sample_id + '_normal',
-    sample=sample_id + '_normal',
-    fastq_1=normal_fastq_1,
-    fastq_2=normal_fastq_2,
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    pl="ILLUMINAL",
-    fasta=fasta,
-    ref_dir=ref_dir,
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
+  if (tumor_deduped_bam != ""){
+    call BQSR.BQSR as tumor_BQSR {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      deduped_bam=tumor_deduped_bam,
+      deduped_bam_index=tumor_deduped_bam_index,
+      db_mills=db_mills,
+      dbmills_dir=dbmills_dir,
+      dbsnp=dbsnp,
+      dbsnp_dir=dbsnp_dir,
+      sample=sample_id + '_tumor',
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
   }
 
-  call Metrics.Metrics as normal_Metrics {
-    input:
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    sorted_bam=normal_mapping.sorted_bam,
-    sorted_bam_index=normal_mapping.sorted_bam_index,
-    sample=sample_id + '_normal',
-    regions=regions,
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
-  }
+  if (normal_fastq_1!= "") {
+    call mapping.mapping as normal_mapping {
+      input: 
+      group=sample_id + '_normal',
+      sample=sample_id + '_normal',
+      fastq_1=normal_fastq_1,
+      fastq_2=normal_fastq_2,
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      pl="ILLUMINAL",
+      fasta=fasta,
+      ref_dir=ref_dir,
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
 
-  call Dedup.Dedup as normal_Dedup {
-    input:
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    sorted_bam=normal_mapping.sorted_bam,
-    sorted_bam_index=normal_mapping.sorted_bam_index,
-    sample=sample_id + '_normal',
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
-  }
+    call Metrics.Metrics as normal_Metrics {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      sorted_bam=normal_mapping.sorted_bam,
+      sorted_bam_index=normal_mapping.sorted_bam_index,
+      sample=sample_id + '_normal',
+      regions=regions,
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
+
+    call Dedup.Dedup as normal_Dedup {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sorted_bam=normal_mapping.sorted_bam,
+      sorted_bam_index=normal_mapping.sorted_bam_index,
+      sample=sample_id + '_normal',
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
 
-  call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
-    input:
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    deduped_bam=normal_Dedup.deduped_bam,
-    deduped_bam_index=normal_Dedup.deduped_bam_index,
-    sample=sample_id + '_normal',
-    regions=regions,
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
+    call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      deduped_bam=normal_Dedup.deduped_bam,
+      deduped_bam_index=normal_Dedup.deduped_bam_index,
+      sample=sample_id + '_normal',
+      regions=regions,
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
+
+    call BQSR.BQSR as normal_BQSR {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      deduped_bam=normal_Dedup.deduped_bam,
+      deduped_bam_index=normal_Dedup.deduped_bam_index,
+      db_mills=db_mills,
+      dbmills_dir=dbmills_dir,
+      dbsnp=dbsnp,
+      dbsnp_dir=dbsnp_dir,
+      sample=sample_id + '_normal',
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
   }
 
-  call BQSR.BQSR as normal_BQSR {
-    input:
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    deduped_bam=normal_Dedup.deduped_bam,
-    deduped_bam_index=normal_Dedup.deduped_bam_index,
-    db_mills=db_mills,
-    dbmills_dir=dbmills_dir,
-    dbsnp=dbsnp,
-    dbsnp_dir=dbsnp_dir,
-    sample=sample_id + '_normal',
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
+  if (normal_deduped_bam != ""){
+    call BQSR.BQSR as normal_BQSR {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      deduped_bam=normal_deduped_bam,
+      deduped_bam_index=normal_deduped_bam_index,
+      db_mills=db_mills,
+      dbmills_dir=dbmills_dir,
+      dbsnp=dbsnp,
+      dbsnp_dir=dbsnp_dir,
+      sample=sample_id + '_normal',
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
   }
 
   if (haplotyper) {