Detect variant

.dockstore.yml

@@ -27,3 +27,57 @@ workflows:
     - name: Gue Su Chang #guesu, gschang
     - name: Irenaeus Chan #IrenaeusChan
     - name: Chad Tomlinson #chad388
+ - subclass: WDL
+   primaryDescriptorPath: /definitions/somatic_wgs.wdl
+   name: somatic_wgs
+   authors:
+    - orcid: 0000-0003-4266-6700 #chrisamiller
+    - orcid: 0000-0002-6388-446X #malachig
+    - orcid: 0000-0003-4378-7328 #susannasiebert
+    - orcid: 0000-0002-0577-4705 #tmooney
+    - orcid: 0000-0001-6293-4632 #sridhar0605
+    - orcid: 0009-0002-2565-0774 #johnegarza
+    - orcid: 0000-0001-7547-5789 #jasonwalker80
+    - orcid: 0000-0003-1928-7139 #zlskidmore
+    - orcid: 0000-0002-7648-1360 #bryanfisk
+    - orcid: 0000-0003-0944-3126 #acoffman
+    - orcid: 0000-0002-2584-5320 #jhundal
+    - orcid: 0000-0002-9704-408X #Matthew-Mosior
+    - orcid: 0000-0002-3024-6891 #apaul7
+    - name: John Maruska #johnmaruska
+    - name: Layth Aljorani #Layth17
+    - name: Sai Mukund Ramakrishnan #saimukund20
+    - name: Feiyu Du #dufeiyu
+    - name: Saad Khan #smk5g5
+    - name: Samuel Peters #sam16711
+    - name: Agata Gruszczynska #GruA
+    - name: Gue Su Chang #guesu, gschang
+    - name: Irenaeus Chan #IrenaeusChan
+    - name: Chad Tomlinson #chad388
+ - subclass: WDL
+   primaryDescriptorPath: /definitions/detect_variants_wgs.wdl
+   name: detect_variants_wgs
+   authors:
+    - orcid: 0000-0003-4266-6700 #chrisamiller
+    - orcid: 0000-0002-6388-446X #malachig
+    - orcid: 0000-0003-4378-7328 #susannasiebert
+    - orcid: 0000-0002-0577-4705 #tmooney
+    - orcid: 0000-0001-6293-4632 #sridhar0605
+    - orcid: 0009-0002-2565-0774 #johnegarza
+    - orcid: 0000-0001-7547-5789 #jasonwalker80
+    - orcid: 0000-0003-1928-7139 #zlskidmore
+    - orcid: 0000-0002-7648-1360 #bryanfisk
+    - orcid: 0000-0003-0944-3126 #acoffman
+    - orcid: 0000-0002-2584-5320 #jhundal
+    - orcid: 0000-0002-9704-408X #Matthew-Mosior
+    - orcid: 0000-0002-3024-6891 #apaul7
+    - name: John Maruska #johnmaruska
+    - name: Layth Aljorani #Layth17
+    - name: Sai Mukund Ramakrishnan #saimukund20
+    - name: Feiyu Du #dufeiyu
+    - name: Saad Khan #smk5g5
+    - name: Samuel Peters #sam16711
+    - name: Agata Gruszczynska #GruA
+    - name: Gue Su Chang #guesu, gschang
+    - name: Irenaeus Chan #IrenaeusChan
+    - name: Chad Tomlinson #chad388

definitions/detect_variants_wgs.wdl

@@ -6,6 +6,7 @@ import "subworkflows/mutect.wdl" as m
 import "subworkflows/strelka_and_post_processing.wdl" as sapp
 import "subworkflows/varscan_pre_and_post_processing.wdl" as vpapp
 import "subworkflows/vcf_readcount_annotator.wdl" as vra
+import "subworkflows/cram_to_bam_and_index.wdl" as cb
 import "tools/add_vep_fields_to_table.wdl" as avftt
 import "tools/bam_readcount.wdl" as br
 import "tools/bgzip.wdl" as b
@@ -22,10 +23,10 @@ workflow detectVariantsWgs {
     File reference
     File reference_fai
     File reference_dict
-    File tumor_bam
-    File tumor_bam_bai
-    File normal_bam
-    File normal_bam_bai
+    File tumor_cram
+    File tumor_cram_index
+    File normal_cram
+    File normal_cram_index
     File roi_intervals
     Boolean strelka_exome_mode
     Int strelka_cpu_reserved = 8
@@ -54,31 +55,52 @@ workflow detectVariantsWgs {
 
     String gnomad_field_name = "gnomADe_AF"  # only change with gnomad_filter_annotation
     Float filter_gnomADe_maximum_population_allele_frequency = 0.001
-    Float filter_mapq0_threshold = 0.15
+    Float filter_mapq0_threshold = 0.10
     Int filter_minimum_depth = 1
     Float? filter_somatic_llr_threshold
     Float? filter_somatic_llr_tumor_purity
     Float? filter_somatic_llr_normal_contamination_rate
     Boolean cle_vcf_filter = false
-    Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"]
+    Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF","LLR"]
     Array[String] variants_to_table_genotype_fields = ["GT", "AD"]
     Array[String] vep_to_table_fields = ["HGVSc", "HGVSp"]
     String tumor_sample_name
     String normal_sample_name
     Array[VepCustomAnnotation] vep_custom_annotations
     File? validated_variants
     File? validated_variants_tbi
+    String prefix # workflow final output prefix
+  }
+
+  call cb.cramTobamAndIndex as tumorConvert {
+    input:
+    reference=reference,
+    reference_index=reference_fai,
+    reference_dict=reference_dict,
+    cram=tumor_cram,
+    cram_index=tumor_cram_index
+
+  }
+
+  call cb.cramTobamAndIndex as normalConvert {
+    input:
+    reference=reference,
+    reference_index=reference_fai,
+    reference_dict=reference_dict,
+    cram=normal_cram,
+    cram_index=normal_cram_index
+
   }
 
   call m.mutect {
     input:
     reference=reference,
     reference_fai=reference_fai,
     reference_dict=reference_dict,
-    tumor_bam=tumor_bam,
-    tumor_bam_bai=tumor_bam_bai,
-    normal_bam=normal_bam,
-    normal_bam_bai=normal_bam_bai,
+    tumor_bam=tumorConvert.indexed_bam,
+    tumor_bam_bai=tumorConvert.indexed_bam_bai,
+    normal_bam=normalConvert.indexed_bam,
+    normal_bam_bai=normalConvert.indexed_bam_bai,
     interval_list=roi_intervals,
     scatter_count=scatter_count,
     tumor_sample_name=tumor_sample_name,
@@ -92,12 +114,12 @@ workflow detectVariantsWgs {
     reference_dict=reference_dict,
 
     tumor_sample_name=tumor_sample_name,
-    tumor_bam=tumor_bam,
-    tumor_bam_bai=tumor_bam_bai,
+    tumor_bam=tumorConvert.indexed_bam,
+    tumor_bam_bai=tumorConvert.indexed_bam_bai,
 
     normal_sample_name=normal_sample_name,
-    normal_bam=normal_bam,
-    normal_bam_bai=normal_bam_bai,
+    normal_bam=normalConvert.indexed_bam,
+    normal_bam_bai=normalConvert.indexed_bam_bai,
 
     interval_list=roi_intervals,
     exome_mode=strelka_exome_mode,
@@ -114,12 +136,12 @@ workflow detectVariantsWgs {
     reference_dict=reference_dict,
 
     tumor_sample_name=tumor_sample_name,
-    tumor_bam=tumor_bam,
-    tumor_bam_bai=tumor_bam_bai,
+    tumor_bam=tumorConvert.indexed_bam,
+    tumor_bam_bai=tumorConvert.indexed_bam_bai,
 
     normal_sample_name=normal_sample_name,
-    normal_bam=normal_bam,
-    normal_bam_bai=normal_bam_bai,
+    normal_bam=normalConvert.indexed_bam,
+    normal_bam_bai=normalConvert.indexed_bam_bai,
 
     interval_list=roi_intervals,
     scatter_count=scatter_count,
@@ -136,11 +158,11 @@ workflow detectVariantsWgs {
     reference_fai=reference_fai,
     reference_dict=reference_dict,
 
-    tumor_bam=tumor_bam,
-    tumor_bam_bai=tumor_bam_bai,
+    tumor_bam=tumorConvert.indexed_bam,
+    tumor_bam_bai=tumorConvert.indexed_bam_bai,
 
-    normal_bam=normal_bam,
-    normal_bam_bai=normal_bam_bai,
+    normal_bam=normalConvert.indexed_bam,
+    normal_bam_bai=normalConvert.indexed_bam_bai,
 
     interval_list=roi_intervals,
     docm_vcf=docm_vcf,
@@ -207,8 +229,8 @@ workflow detectVariantsWgs {
     reference_fai=reference_fai,
     reference_dict=reference_dict,
     sample=tumor_sample_name,
-    bam=tumor_bam,
-    bam_bai=tumor_bam_bai,
+    bam=tumorConvert.indexed_bam,
+    bam_bai=tumorConvert.indexed_bam_bai,
     min_base_quality=readcount_minimum_base_quality,
     min_mapping_quality=readcount_minimum_mapping_quality
   }
@@ -220,8 +242,8 @@ workflow detectVariantsWgs {
     reference_fai=reference_fai,
     reference_dict=reference_dict,
     sample=normal_sample_name,
-    bam=normal_bam,
-    bam_bai=normal_bam_bai,
+    bam=normalConvert.indexed_bam,
+    bam_bai=normalConvert.indexed_bam_bai,
     min_base_quality=readcount_minimum_base_quality,
     min_mapping_quality=readcount_minimum_mapping_quality
   }
@@ -258,8 +280,8 @@ workflow detectVariantsWgs {
     filter_somatic_llr_tumor_purity=filter_somatic_llr_tumor_purity,
     filter_somatic_llr_normal_contamination_rate=filter_somatic_llr_normal_contamination_rate,
     filter_minimum_depth=filter_minimum_depth,
-    tumor_bam=tumor_bam,
-    tumor_bam_bai=tumor_bam_bai,
+    tumor_bam=tumorConvert.indexed_bam,
+    tumor_bam_bai=tumorConvert.indexed_bam_bai,
     do_cle_vcf_filter=cle_vcf_filter,
     reference=reference,
     reference_fai=reference_fai,
@@ -294,7 +316,8 @@ workflow detectVariantsWgs {
     input:
     vcf=annotatedFilterIndex.indexed_vcf,
     tsv=variantsToTable.variants_tsv,
-    vep_fields=vep_to_table_fields
+    vep_fields=vep_to_table_fields,
+    prefix=prefix
   }
 
   output {

definitions/somatic_wgs.wdl

@@ -177,10 +177,10 @@ workflow somaticWgs {
     reference=reference,
     reference_fai=reference_fai,
     reference_dict=reference_dict,
-    tumor_bam=tumorAlignment.final_bam,
-    tumor_bam_bai=tumorAlignment.final_bam_bai,
-    normal_bam=normalAlignment.final_bam,
-    normal_bam_bai=normalAlignment.final_bam_bai,
+    tumor_cram=tumorAlignment.final_bam,
+    tumor_cram_index=tumorAlignment.final_bam_bai,
+    normal_cram=normalAlignment.final_bam,
+    normal_cram_index=normalAlignment.final_bam_bai,
     roi_intervals=target_intervals,
     strelka_exome_mode=false,
     strelka_cpu_reserved=strelka_cpu_reserved,

definitions/subworkflows/cram_to_bam_and_index.wdl

@@ -0,0 +1,33 @@
+version 1.0
+
+import "../tools/cram_to_bam.wdl" as cb
+import "../tools/index_bam.wdl" as i
+
+workflow cramTobamAndIndex{
+    input {
+        File cram
+        File cram_index
+        File reference
+        File reference_index
+        File reference_dict
+    }
+
+    call cb.cramToBam {
+        input:
+        cram=cram,
+        cram_index=cram_index,
+        reference=reference,
+        reference_index=reference_index,
+        reference_dict=reference_dict
+    }
+
+    call i.indexBam {
+        input: bam=cramToBam.bam
+    }
+
+    output {
+        File indexed_bam = indexBam.indexed_bam
+        File indexed_bam_bai = indexBam.indexed_bam_bai
+        File indexed_bai = indexBam.indexed_bai
+    }
+}

definitions/tools/cram_to_bam.wdl

@@ -9,9 +9,9 @@ task cramToBam {
     File reference_dict
   }
 
-  Int space_needed_gb = 10 + round(size([cram, cram_index, reference, reference_index, reference_dict], "GB") * 3)
+  Int space_needed_gb = 10 + round(size([cram, cram_index, reference, reference_index, reference_dict], "GB") * 5)
   runtime {
-    memory: "4GB"
+    memory: "8GB"
     docker: "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
     disks: "local-disk ~{space_needed_gb} HDD"
   }

definitions/tools/docm_gatk_haplotype_caller.wdl

@@ -27,7 +27,7 @@ task docmGatkHaplotypeCaller {
     preemptible: 1
     maxRetries: 2
     memory: "9GB"
-    docker: "broadinstitute/gatk:4.1.2.0"
+    docker: "broadinstitute/gatk:4.1.3.0"
     disks: "local-disk ~{space_needed_gb} HDD"
   }
 

definitions/tools/mutect.wdl

@@ -29,7 +29,7 @@ task mutect {
     preemptible: 1
     maxRetries: 2
     docker: "broadinstitute/gatk:4.2.3.0"
-    memory: "2GB"
+    memory: "8GB"
     bootDiskSizeGb: space_needed_gb
     disks: "local-disk ~{space_needed_gb} HDD"
   }