Removed unused task from HaplotypeCaller_Simplified.wdl

Author: jonn-smith

wdl/tasks/VariantCalling/HaplotypeCaller_Simplified.wdl

@@ -251,136 +251,3 @@ task HaplotypeCaller_GATK4_VCF {
         docker:                 select_first([runtime_attr.docker,            default_attr.docker])
     }
 }
-
-
-# This task is here because merging bamout files using Picard produces an error.
-task MergeBamouts {
-
-    input {
-        Array[File] bams
-        String prefix
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    Int disk_size = ceil(size(bams, "GiB") * 2) + 10
-
-    command <<<
-
-        set -euxo pipefail
-
-        # Make sure we use all our processors:
-        np=$(cat /proc/cpuinfo | grep ^processor | tail -n1 | awk '{print $NF+1}')
-
-        ithreads=${np}
-
-        # If the number of processors = 1, then `let` will return 1 here:
-        # So we need to turn off `set -e` for this command:
-        set +e
-        mthreads=$((np-1))
-        set -e
-
-        samtools merge -@${mthreads} ~{prefix}.bam ~{sep=" " bams}
-        samtools index -@${ithreads} ~{prefix}.bam
-        mv ~{prefix}.bam.bai ~{prefix}.bai
-    >>>
-
-    #########################
-    RuntimeAttr default_attr = object {
-       cpu_cores:          1,
-       mem_gb:             4,
-       disk_gb:            disk_size,
-       boot_disk_gb:       25,
-       preemptible_tries:  1,
-       max_retries:        1,
-       docker:             "us.gcr.io/broad-dsp-lrma/lr-basic:0.1.1"
-    }
-
-    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])
-    }
-
-    output {
-        File output_bam = "~{prefix}.bam"
-        File output_bam_index = "~{prefix}.bai"
-    }
-}
-
-task ReblockGVCF {
-
-    input {
-        File gvcf
-        File gvcf_index
-
-        File ref_fasta
-        File ref_fasta_fai
-        File ref_dict
-
-        String prefix
-
-        Array[Int] gq_blocks = [20, 30, 40]
-
-        Float? tree_score_cutoff
-
-        Array[String]? annotations_to_keep
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    Int disk_size = ceil((size(gvcf, "GiB") * 4) + size(ref_fasta, "GiB") + size(ref_fasta_fai, "GiB") + size(ref_dict, "GiB") + 10)
-
-    String annotations_to_keep_arg = if defined(annotations_to_keep) then "--annotations-to-keep" else ""
-
-    command {
-        set -euxo pipefail
-
-        gatk --java-options "-Xms3000m -Xmx3000m" \
-            ReblockGVCF \
-                -R ~{ref_fasta} \
-                -V ~{gvcf} \
-                -do-qual-approx \
-                -G StandardAnnotation -G StandardHCAnnotation  \
-                -A AssemblyComplexity \
-                --annotate-with-num-discovered-alleles \
-                --floor-blocks \
-                -GQB ~{sep=" -GQB " gq_blocks} \
-                ~{"--tree-score-threshold-to-no-call " + tree_score_cutoff} \
-                ~{annotations_to_keep_arg} ~{sep=" --annotations-to-keep " annotations_to_keep} \
-                -O ~{prefix}.rb.g.vcf.gz
-    }
-
-    #########################
-    RuntimeAttr default_attr = object {
-       cpu_cores:          2,
-       mem_gb:             4,
-       disk_gb:            disk_size,
-       boot_disk_gb:       25,
-       preemptible_tries:  1,
-       max_retries:        1,
-       docker:             "broadinstitute/gatk-nightly:2024-04-16-4.5.0.0-25-g986cb1549-NIGHTLY-SNAPSHOT"
-    }
-    # TODO: Fix this docker image to a stable version after the next GATK release!
-
-    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])
-    }
-
-    output {
-        File output_gvcf = "~{prefix}.rb.g.vcf.gz"
-        File output_gvcf_index = "~{prefix}.rb.g.vcf.gz.tbi"
-    }
-}