Add TRGT Special-purpose caller

docker/lr-trgt/Dockerfile

@@ -0,0 +1,39 @@
+FROM ubuntu:22.04
+
+RUN apt-get update && \
+        apt-get install -y wget bzip2 gcc g++ zlib1g-dev libbz2-dev make ncurses-dev liblzma-dev libcurl4-openssl-dev libssl-dev
+
+RUN wget "https://github.com/PacificBiosciences/trgt/releases/download/v1.0.0/trgt-v1.0.0-x86_64-unknown-linux-gnu.tar.gz" -O "trgt.tar.gz" && \
+        tar -zxvf trgt.tar.gz && \
+        chmod 777 trgt-v1.0.0-x86_64-unknown-linux-gnu/trgt && \
+        mv trgt-v1.0.0-x86_64-unknown-linux-gnu/trgt /usr/bin/ && \
+        rm -r trgt-v1.0.0-x86_64-unknown-linux-gnu/
+
+RUN wget "https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2" && \
+        bunzip2 bcftools-1.20.tar.bz2 && \
+        tar -xvf bcftools-1.20.tar && \
+        cd bcftools-1.20/ && \
+        ./configure && \
+        make && \
+        make install && \
+        cd .. && \
+        rm -r bcftools-1.20/ && \
+        rm bcftools-1.20.tar
+
+RUN wget "https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2" && \
+        bunzip2 htslib-1.20.tar.bz2 && \
+        tar -xvf htslib-1.20.tar && \
+        cd htslib-1.20/ && \
+        ./configure && \
+        make && \
+        make install && \
+        cd .. && \
+        rm -r htslib-1.20/ && \
+        rm htslib-1.20.tar
+
+RUN wget "https://zuchnerlab.s3.amazonaws.com/RepeatExpansions/TRGT/adotto_TRregions_TRGTFormatWithFlankingSeq_v1.0_under1kb.bed.gz" && \
+        gunzip adotto_TRregions_TRGTFormatWithFlankingSeq_v1.0_under1kb.bed.gz
+
+RUN wget "https://zuchnerlab.s3.amazonaws.com/RepeatExpansions/TRGT/T2T/CHM13.adotto_TRregions_TRGTFormatWithFlankingSeq_v1.0_under1kb.bed.gz" && \
+        gunzip CHM13.adotto_TRregions_TRGTFormatWithFlankingSeq_v1.0_under1kb.bed.gz
+

docker/lr-trgt/Makefile

@@ -0,0 +1,15 @@
+VERSION = 1.0.0
+TAG1 = us.gcr.io/broad-dsp-lrma/lr-trgt:$(VERSION)
+TAG2 = us.gcr.io/broad-dsp-lrma/lr-trgt:latest
+
+all: build push
+
+build:
+        docker build -t $(TAG1) -t $(TAG2) .
+
+build_no_cache:
+        docker build --no-cache -t $(TAG1) -t $(TAG2) .
+
+push:
+        docker push $(TAG1)
+        docker push $(TAG2)

wdl/pipelines/PacBio/VariantCalling/PBCCSWholeGenome.wdl

@@ -4,7 +4,6 @@ import "../../../tasks/Utility/PBUtils.wdl" as PB
 import "../../../tasks/Utility/Utils.wdl" as Utils
 import "../../../tasks/VariantCalling/CallVariantsPBCCS.wdl" as VAR
 import "../../../tasks/Utility/Finalize.wdl" as FF
-
 import "../../../tasks/QC/SampleLevelAlignedMetrics.wdl" as COV
 
 workflow PBCCSWholeGenome {
@@ -31,6 +30,9 @@ workflow PBCCSWholeGenome {
         run_dv_pepper_analysis:  "to turn on DV-Pepper analysis or not (non-trivial increase in cost and runtime)"
         ref_scatter_interval_list_locator: "A file holding paths to interval_list files; needed only when running DV-Pepper"
         ref_scatter_interval_list_ids:     "A file that gives short IDs to the interval_list files; needed only when running DV-Pepper"
+
+        call_trs: "whether to call TRs"
+        trs_catalog: "optionally specify a non-default catalog to use when calling TRs, for use with TRGT"
     }
 
     input {

wdl/pipelines/PacBio/VariantCalling/PBCCS_CallTRs.wdl

@@ -0,0 +1,45 @@
+version 1.0
+
+import "../../../tasks/VariantCalling/TRGT.wdl" as TRGT
+import "../../../structs/Structs.wdl"
+
+workflow runTRGT {
+
+  meta {
+    description: "Uses TRGT to size TRs in a bam file."
+  }
+
+  input {
+    File input_bam
+    File input_bam_bai
+    String basename = basename(input_bam, ".bam")
+    String output_gs_path
+    File ref_fasta
+    File ref_fasta_index
+    String repeatCatalog
+    Int is_female # 1=female; 0=male
+    Int cpuCores = 16
+
+    #Optional runtime arguments
+    RuntimeAttr? runtime_attr_override
+  }
+
+  call TRGT.processWithTRGT as processWithTRGT {
+    input:
+      input_bam = input_bam,
+      input_bam_bai = input_bam_bai,
+      basename = basename,
+      ref_fasta = ref_fasta,
+      ref_fasta_index = ref_fasta_index,
+      repeatCatalog = repeatCatalog,
+      is_female = is_female,
+      cpuCores = cpuCores,
+      runtime_attr_override = runtime_attr_override
+  }
+
+  output {
+    File trgt_output_vcf = processWithTRGT.trgt_output_vcf
+    File trgt_output_vcf_idx = processWithTRGT.trgt_output_vcf_idx
+    File trgt_output_bam = processWithTRGT.trgt_output_bam
+  }
+}

wdl/pipelines/PacBio/VariantCalling/PBCCS_CallTRs_exampleInputs_GRCh38.json

@@ -0,0 +1,9 @@
+{
+  "runTRGT.input_bam": "gs://fc-7891e5cf-0a7a-4c2f-8a18-0d05b27c53ab/T2T/PBCCSWholeGenome/NA19240/alignments/NA19240.bam",
+  "runTRGT.input_bam_bai": "gs://fc-7891e5cf-0a7a-4c2f-8a18-0d05b27c53ab/T2T/PBCCSWholeGenome/NA19240/alignments/NA19240.bam.bai",
+  "runTRGT.output_gs_path": "gs://fc-c1de2dd5-0f83-49c8-84ee-0f153c4d0a59/TRGT/GRCh38/",
+  "runTRGT.ref_fasta": "gs://fc-c1de2dd5-0f83-49c8-84ee-0f153c4d0a59/resources/GRCh38_full_analysis_set_plus_decoy_hla.fa",
+  "runTRGT.ref_fasta_index": "gs://fc-c1de2dd5-0f83-49c8-84ee-0f153c4d0a59/resources/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai",
+  "runTRGT.repeatCatalog": "/GRCh38.adotto_TRregions_TRGTFormatWithFlankingSeq_v1.0_under1kb.bed",
+  "runTRGT.is_female": 1
+}

wdl/pipelines/PacBio/VariantCalling/PBCCS_CallTRs_exampleInputs_T2T.json

@@ -0,0 +1,9 @@
+{
+  "runTRGT.input_bam": "gs://fc-7891e5cf-0a7a-4c2f-8a18-0d05b27c53ab/T2T/PBCCSWholeGenome/NA19240/alignments/NA19240.bam",
+  "runTRGT.input_bam_bai": "gs://fc-7891e5cf-0a7a-4c2f-8a18-0d05b27c53ab/T2T/PBCCSWholeGenome/NA19240/alignments/NA19240.bam.bai",
+  "runTRGT.output_gs_path": "gs://fc-c1de2dd5-0f83-49c8-84ee-0f153c4d0a59/TRGT/T2T/",
+  "runTRGT.ref_fasta": "gs://fc-c1de2dd5-0f83-49c8-84ee-0f153c4d0a59/resources/chm13v2.0.ebv.fa",
+  "runTRGT.ref_fasta_index": "gs://fc-c1de2dd5-0f83-49c8-84ee-0f153c4d0a59/resources/chm13v2.0.ebv.fa.fai",
+  "runTRGT.repeatCatalog": "/CHM13.adotto_TRregions_TRGTFormatWithFlankingSeq_v1.0_under1kb.bed",
+  "runTRGT.is_female": 1
+}

wdl/tasks/VariantCalling/TRGT.wdl

@@ -0,0 +1,62 @@
+version 1.0
+
+import "../../structs/Structs.wdl"
+
+task processWithTRGT {
+  input {
+    File input_bam
+    File input_bam_bai
+    String basename
+    File ref_fasta
+    File ref_fasta_index
+    String repeatCatalog
+    Int is_female # 1=female, 0=male
+    Int cpuCores = 16
+
+    RuntimeAttr? runtime_attr_override
+
+  }
+
+  meta {
+    description: "Uses TRGT to size TRs in a bam file."
+  }
+
+  command <<<
+    set -euo pipefail
+    karyotype="XY"
+    if [[ ~{is_female} -eq 1 ]]; then karyotype="XX"; fi 
+    trgt genotype --genome ~{ref_fasta} --repeats ~{repeatCatalog} --reads ~{input_bam} --threads ~{cpuCores} --output-prefix ~{basename}_trgt --karyotype ${karyotype}
+    bcftools sort -Ob -o ~{basename}_trgt_sorted.vcf.gz ~{basename}_trgt.vcf.gz
+    mv ~{basename}_trgt_sorted.vcf.gz ~{basename}_trgt.vcf.gz
+    bcftools index -t ~{basename}_trgt.vcf.gz
+
+  >>>
+
+  output {
+    File trgt_output_vcf = "~{basename}_trgt.vcf.gz"
+    File trgt_output_vcf_idx = "~{basename}_trgt.vcf.gz.tbi"
+    File trgt_output_bam = "~{basename}_trgt.spanning.bam"
+  }
+
+  #########################
+  RuntimeAttr default_attr = object {
+      cpu_cores:          cpuCores,
+      mem_gb:             16,
+      disk_gb:            500,
+      boot_disk_gb:       10,
+      preemptible_tries:  3,
+      max_retries:        1,
+      docker:             "us.gcr.io/broad-dsp-lrma/lr-trgt:1.0.0"
+  }
+  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]) + " 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])
+      docker:                 select_first([runtime_attr.docker,            default_attr.docker])
+  }
+}