add shapeit4 pipeline for hidive experiment

wdl/pipelines/TechAgnostic/Phasing/Shapeit4Hidive.wdl

@@ -0,0 +1,179 @@
+version 1.0
+
+workflow Shapeit4Hidive {   
+
+    input {
+        File joint_vcf
+        File joint_vcf_tbi
+        File genetic_mapping_tsv_for_shapeit4
+        File regionlist
+        File chromosomelist
+        Int shapeit4_num_threads
+        Int shapeit4_memory
+        String shapeit4_extra_args
+        String output_prefix
+
+    }
+
+    Map[String, String] genetic_mapping_dict = read_map(genetic_mapping_tsv_for_shapeit4)
+
+    Array[String] region_list = read_lines(regionlist)
+
+    Array[String] chromosome_list = read_lines(chromosomelist)
+
+    scatter (j in range(length(region_list))) {
+        String chromosome = chromosome_list[j]
+        call Shapeit4 { input:
+            vcf_input = joint_vcf,
+            vcf_index = joint_vcf_tbi,
+            mappingfile = genetic_mapping_dict[chromosome],
+            region = region_list[j],
+            prefix = output_prefix + "." + chromosome + ".shard-" + j + ".phased",
+            num_threads = shapeit4_num_threads,
+            memory = shapeit4_memory,
+            extra_args = shapeit4_extra_args
+        }
+    }
+
+    call LigateVcfs { input:
+        vcfs = Shapeit4.phased_bcf,
+        prefix = output_prefix + "." + ".phased.ligated"
+    }
+
+    output {
+
+        File phased_vcf_gz = LigateVcfs.ligated_vcf_gz
+        File phased_vcf_gz_tbi = LigateVcfs.ligated_vcf_gz_tbi
+
+        }
+}
+
+struct RuntimeAttr {
+    Float? mem_gb
+    Int? cpu_cores
+    Int? disk_gb
+    Int? boot_disk_gb
+    Int? preemptible_tries
+    Int? max_retries
+    String? docker
+}
+
+struct DataTypeParameters {
+    Int num_shards
+    String map_preset
+}
+
+
+task LigateVcfs {
+
+    input {
+        Array[File] vcfs
+        Array[File]? vcf_idxs
+        String prefix
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    Int disk_size = 2*ceil(size(vcfs, "GB")) + 1
+
+    command <<<
+        set -euxo pipefail
+        if ! ~{defined(vcf_idxs)}; then
+            for ff in ~{sep=' ' vcfs}; do bcftools index $ff; done
+        fi
+
+        wget https://github.com/odelaneau/shapeit5/releases/download/v5.1.1/ligate_static
+        chmod +x ligate_static
+
+        ./ligate_static --input ~{write_lines(vcfs)} --output ~{prefix}.vcf.gz
+        bcftools index -t ~{prefix}.vcf.gz
+    >>>
+
+    output {
+        File ligated_vcf_gz = "~{prefix}.vcf.gz"
+        File ligated_vcf_gz_tbi = "~{prefix}.vcf.gz.tbi"
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          2,
+        mem_gb:             8,
+        disk_gb:            disk_size,
+        boot_disk_gb:       10,
+        preemptible_tries:  2,
+        max_retries:        1,
+        docker:"us.gcr.io/broad-dsp-lrma/lr-gcloud-samtools:0.1.2"
+    }
+    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]) + " SSD"
+        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])
+    }
+}
+
+task Shapeit4 {
+    input{
+        File vcf_input
+        File vcf_index
+        File mappingfile
+        String region
+        String prefix
+        Int num_threads
+        Int memory
+        String extra_args
+
+        RuntimeAttr? runtime_attr_override
+        String zones = "us-central1-a us-central1-b us-central1-c us-central1-f"
+    }
+    command <<<
+        # add AN AC tag
+
+        # export MONITOR_MOUNT_POINT="/cromwell_root/"
+        # bash /opt/vm_local_monitoring_script.sh &> resources.log &
+        # job_id=$(ps -aux | grep -F 'vm_local_monitoring_script.sh' | head -1 | awk '{print $2}')
+
+        shapeit4.2 --input ~{vcf_input} \
+                --map ~{mappingfile} \
+                --region ~{region} \
+                --sequencing \
+                --output ~{prefix}.bcf \
+                --thread ~{num_threads} \
+                ~{extra_args}
+
+        # if ps -p "${job_id}" > /dev/null; then kill "${job_id}"; fi
+    >>>
+
+    output{
+        # File resouce_monitor_log = "resources.log"
+        File phased_bcf = "~{prefix}.bcf"
+    }
+
+    #Int disk_size = 100 + ceil(2 * size(vcf_input, "GiB"))
+
+ #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          num_threads,
+        mem_gb:             memory,
+        disk_gb:            100,
+        boot_disk_gb:       100,
+        preemptible_tries:  0,
+        max_retries:        0,
+        docker:             "hangsuunc/shapeit4:v1"
+    }
+    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]) + " SSD"
+        zones: zones
+        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])
+    }
+}