diff --git a/docker/lr-metrics/environment.yml b/docker/lr-metrics/environment.yml
index 1414228d8..fdc08c739 100644
--- a/docker/lr-metrics/environment.yml
+++ b/docker/lr-metrics/environment.yml
@@ -5,6 +5,7 @@ channels:
   - bioconda
   - r
 dependencies:
+  - conda-forge::ncurses
   - samtools
   - bedtools
   - java-jdk
diff --git a/docker/lr-mini/Dockerfile b/docker/lr-mini/Dockerfile
new file mode 100644
index 000000000..096dab081
--- /dev/null
+++ b/docker/lr-mini/Dockerfile
@@ -0,0 +1,14 @@
+FROM us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2023-07-28-v0.28.1-beta-e70dfbd7
+
+#install some small, commonly used tools
+RUN apt-get -qqy update --fix-missing && \
+    apt-get -qqy dist-upgrade && \
+    apt-get -qqy install --no-install-recommends bsdmainutils datamash tree && \
+    apt-get -qqy clean && \
+    rm -rf /tmp/* \
+           /var/tmp/* \
+           /var/cache/apt/* \
+           /var/lib/apt/lists/* \
+           /usr/share/man/?? \
+           /usr/share/man/??_*
+
diff --git a/docker/lr-mini/Makefile b/docker/lr-mini/Makefile
new file mode 100644
index 000000000..7d4253440
--- /dev/null
+++ b/docker/lr-mini/Makefile
@@ -0,0 +1,17 @@
+IMAGE_NAME = lr-mini
+VERSION = 0.1.1
+
+TAG1 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):$(VERSION)
+TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):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 $(TAG2)
diff --git a/docker/lr-mosdepth/Dockerfile b/docker/lr-mosdepth/Dockerfile
index 9a5acff9d..77232063e 100644
--- a/docker/lr-mosdepth/Dockerfile
+++ b/docker/lr-mosdepth/Dockerfile
@@ -10,7 +10,7 @@ RUN conda env create -f /environment.yml && conda clean -a
 ENV PATH=/opt/conda/envs/lr-mosdepth/bin/:/root/google-cloud-sdk/bin/:${PATH}
 
 RUN apt-get -y update && \
-    apt-get -y install curl zlib1g-dev libcurl4-openssl-dev libbz2-dev liblzma-dev && \
+    apt-get -y install curl zlib1g-dev libcurl4-openssl-dev libbz2-dev liblzma-dev datamash bsdmainutils && \
     apt-get clean
 
 # install gsutil
diff --git a/docker/lr-mosdepth/Makefile b/docker/lr-mosdepth/Makefile
index 9b2693d2b..0186202bd 100644
--- a/docker/lr-mosdepth/Makefile
+++ b/docker/lr-mosdepth/Makefile
@@ -1,5 +1,5 @@
 IMAGE_NAME = lr-mosdepth
-VERSION = 0.3.1 # This should match the MosDepth version number
+VERSION = 0.3.2 # This should match the MosDepth version number
 
 TAG1 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):$(VERSION)
 TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):latest
diff --git a/wdl/deprecated/ONT10x.wdl b/wdl/deprecated/ONT10x.wdl
index 8ce3068ea..f9a260b5d 100644
--- a/wdl/deprecated/ONT10x.wdl
+++ b/wdl/deprecated/ONT10x.wdl
@@ -1,10 +1,10 @@
 version 1.0
 
+import "../structs/Structs.wdl"
 import "../tasks/Utility/Utils.wdl" as Utils
 import "../tasks/Utility/ONTUtils.wdl" as ONT
 import "tasks/C3POa.wdl" as C3
 import "../tasks/Alignment/AlignReads.wdl" as AR
-import "../tasks/QC/AlignedMetrics.wdl" as AM
 import "../tasks/Utility/Finalize.wdl" as FF
 
 workflow ONT10x {
diff --git a/wdl/deprecated/PBCCS10x.wdl b/wdl/deprecated/PBCCS10x.wdl
index 7b54cf212..d1658c393 100644
--- a/wdl/deprecated/PBCCS10x.wdl
+++ b/wdl/deprecated/PBCCS10x.wdl
@@ -2,7 +2,6 @@ version 1.0
 
 import "../tasks/Utility/PBUtils.wdl" as PB
 import "../tasks/Utility/Utils.wdl" as Utils
-import "../tasks/Alignment/AlignReads.wdl" as AR
 import "../tasks/QC/AlignedMetrics.wdl" as AM
 import "tasks/AnnotateAdapters.wdl" as AA
 import "../tasks/Utility/Finalize.wdl" as FF
diff --git a/wdl/deprecated/PBCCSDemultiplexWholeGenome.wdl b/wdl/deprecated/PBCCSDemultiplexWholeGenome.wdl
index 05a41636e..edf05806d 100644
--- a/wdl/deprecated/PBCCSDemultiplexWholeGenome.wdl
+++ b/wdl/deprecated/PBCCSDemultiplexWholeGenome.wdl
@@ -10,7 +10,6 @@ version 1.0
 
 import "../tasks/Utility/PBUtils.wdl" as PB
 import "../tasks/Utility/Utils.wdl" as Utils
-import "../tasks/Alignment/AlignReads.wdl" as AR
 import "../tasks/QC/AlignedMetrics.wdl" as AM
 import "../tasks/VariantCalling/CallVariantsPBCCS.wdl" as VAR
 import "../tasks/Utility/Finalize.wdl" as FF
diff --git a/wdl/deprecated/PBCLRDemultiplexWholeGenome.wdl b/wdl/deprecated/PBCLRDemultiplexWholeGenome.wdl
index 764a2ac55..429628a0d 100644
--- a/wdl/deprecated/PBCLRDemultiplexWholeGenome.wdl
+++ b/wdl/deprecated/PBCLRDemultiplexWholeGenome.wdl
@@ -8,7 +8,6 @@ version 1.0
 
 import "../tasks/Utility/PBUtils.wdl" as PB
 import "../tasks/Utility/Utils.wdl" as Utils
-import "../tasks/Alignment/AlignReads.wdl" as AR
 import "../tasks/QC/AlignedMetrics.wdl" as AM
 import "../tasks/Utility/Finalize.wdl" as FF
 
diff --git a/wdl/deprecated/tasks/C3POa.wdl b/wdl/deprecated/tasks/C3POa.wdl
index 1d82029a5..467c80d37 100644
--- a/wdl/deprecated/tasks/C3POa.wdl
+++ b/wdl/deprecated/tasks/C3POa.wdl
@@ -1,7 +1,6 @@
 version 1.0
 
 import "../../structs/Structs.wdl"
-import "../../tasks/Utility/Utils.wdl" as Utils
 
 workflow C3POa {
     input {
diff --git a/wdl/deprecated/tasks/GATKBestPractice.wdl b/wdl/deprecated/tasks/GATKBestPractice.wdl
index 412ef5fdc..e38d24633 100644
--- a/wdl/deprecated/tasks/GATKBestPractice.wdl
+++ b/wdl/deprecated/tasks/GATKBestPractice.wdl
@@ -8,6 +8,7 @@ version 1.0
 # "https://github.com/PacificBiosciences/hg002-ccs/"
 ##########################################################################################
 
+import "../../structs/Structs.wdl"
 import "dsde_pipelines_tasks/GermlineVariantDiscovery.wdl" as Calling
 import "dsde_pipelines_tasks/Qc.wdl" as QC
 import "dsde_pipelines_tasks/Utilities.wdl" as DSDEPipelinesUtils
diff --git a/wdl/deprecated/tasks/Scrapbook.wdl b/wdl/deprecated/tasks/Scrapbook.wdl
new file mode 100644
index 000000000..c186e875b
--- /dev/null
+++ b/wdl/deprecated/tasks/Scrapbook.wdl
@@ -0,0 +1,185 @@
+version 1.0
+
+import "../../structs/Structs.wdl"
+
+task CoverageTrack {
+    input {
+        File bam
+        File bai
+        String chr
+        String start
+        String end
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    String basename = basename(bam, ".bam")
+    Int disk_size = 2*ceil(size(bam, "GB") + size(bai, "GB"))
+
+    command <<<
+        set -euxo pipefail
+
+        samtools depth -a ~{bam} -r ~{chr}:~{start}-~{end} | bgzip > ~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz
+        tabix -p bed ~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz
+    >>>
+
+    output {
+        File coverage = "~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz"
+        File coverage_tbi = "~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz.tbi"
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          1,
+        mem_gb:             4,
+        disk_gb:            disk_size,
+        boot_disk_gb:       10,
+        preemptible_tries:  2,
+        max_retries:        1,
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
+    }
+    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])
+    }
+}
+
+task FilterMQ0Reads {
+    input {
+        File bam
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    Int disk_size = 2*ceil(size(bam, "GB"))
+    String prefix = basename(bam, ".bam")
+
+    command <<<
+        set -euxo pipefail
+
+        samtools view -q 1 -b ~{bam} > ~{prefix}.no_mq0.bam
+        samtools index ~{prefix}.no_mq0.bam
+    >>>
+
+    output {
+        File no_mq0_bam = "~{prefix}.no_mq0.bam"
+        File no_mq0_bai = "~{prefix}.no_mq0.bam.bai"
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          1,
+        mem_gb:             2,
+        disk_gb:            disk_size,
+        boot_disk_gb:       10,
+        preemptible_tries:  2,
+        max_retries:        1,
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
+    }
+    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])
+    }
+}
+
+task ComputeBedCoverage {
+    input {
+        File bam
+        File bai
+        File bed
+        String prefix
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    Int disk_size = 2*ceil(size(bam, "GB") + size(bai, "GB") + size(bed, "GB"))
+
+    command <<<
+        set -euxo pipefail
+
+        bedtools coverage -b ~{bed} -a ~{bam} -nobuf | gzip > ~{prefix}.txt.gz
+        zcat ~{prefix}.txt.gz | awk '{ sum += sprintf("%f", $15*$16) } END { printf("%f\n", sum) }' > ~{prefix}.count.txt
+    >>>
+
+    output {
+        File coverage = "~{prefix}.txt.gz"
+        Float counts = read_float("~{prefix}.count.txt")
+        File counts_file = "~{prefix}.count.txt"
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          1,
+        mem_gb:             2,
+        disk_gb:            disk_size,
+        boot_disk_gb:       10,
+        preemptible_tries:  2,
+        max_retries:        1,
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
+    }
+    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])
+    }
+}
+
+task BamToBed {
+    input {
+        File bam
+        File bai
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    String bed = basename(bam, ".bam") + ".bed"
+    Int disk_size = 4*ceil(size(bam, "GB") + size(bai, "GB"))
+
+    command <<<
+        set -euxo pipefail
+
+        bedtools bamtobed -i ~{bam} > ~{bed}
+    >>>
+
+    output {
+        File bedfile = bed
+    }
+
+    #########################
+    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-metrics:0.1.11"
+    }
+    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])
+    }
+}
diff --git a/wdl/pipelines/ONT/Epigenomics/ONTMethylation.wdl b/wdl/pipelines/ONT/Epigenomics/ONTMethylation.wdl
index c7cff9978..d7b4237bc 100644
--- a/wdl/pipelines/ONT/Epigenomics/ONTMethylation.wdl
+++ b/wdl/pipelines/ONT/Epigenomics/ONTMethylation.wdl
@@ -1,9 +1,8 @@
 version 1.0
 
+import "../../../structs/Structs.wdl"
 import "../../../tasks/Utility/Utils.wdl" as Utils
-import "../../../tasks/Utility/ONTUtils.wdl" as ONTUtils
 import "../../../tasks/Utility/VariantUtils.wdl"
-import "../../../tasks/Preprocessing/Guppy.wdl" as Guppy
 import "../../../tasks/Utility/Finalize.wdl" as FF
 
 workflow ONTMethylation {
@@ -733,4 +732,4 @@ task CallHaploidVariants {
         maxRetries:             select_first([runtime_attr.max_retries,       default_attr.max_retries])
         docker:                 select_first([runtime_attr.docker,            default_attr.docker])
     }
-}
\ No newline at end of file
+}
diff --git a/wdl/pipelines/ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl b/wdl/pipelines/ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl
index ed387effa..d4d49ac48 100644
--- a/wdl/pipelines/ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl
+++ b/wdl/pipelines/ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl
@@ -1,7 +1,6 @@
 version 1.0
 
 import "../../../structs/Structs.wdl"
-import "../../../tasks/Utility/Finalize.wdl" as FF
 
 workflow ONTPfHrp2Hrp3Status {
 
@@ -86,7 +85,7 @@ task IsLocusDeleted {
         boot_disk_gb:       10,
         preemptible_tries:  2,
         max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-mosdepth:0.3.1"
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-mosdepth:0.3.2"
     }
     RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
     runtime {
diff --git a/wdl/pipelines/ONT/Preprocessing/ONTBasecall.wdl b/wdl/pipelines/ONT/Preprocessing/ONTBasecall.wdl
index 8173fcf4e..8d09fe9fb 100644
--- a/wdl/pipelines/ONT/Preprocessing/ONTBasecall.wdl
+++ b/wdl/pipelines/ONT/Preprocessing/ONTBasecall.wdl
@@ -1,7 +1,6 @@
 version 1.0
 
 import "../../../tasks/Preprocessing/Guppy.wdl" as Guppy
-import "../../../tasks/Utility/Finalize.wdl" as FF
 
 workflow ONTBasecall {
 
diff --git a/wdl/pipelines/ONT/VariantCalling/ONTWholeGenome.wdl b/wdl/pipelines/ONT/VariantCalling/ONTWholeGenome.wdl
index 7e0470bfb..be29a30b9 100644
--- a/wdl/pipelines/ONT/VariantCalling/ONTWholeGenome.wdl
+++ b/wdl/pipelines/ONT/VariantCalling/ONTWholeGenome.wdl
@@ -1,6 +1,5 @@
 version 1.0
 
-import "../../../tasks/Utility/ONTUtils.wdl" as ONT
 import "../../../tasks/Utility/Utils.wdl" as Utils
 import "../../../tasks/VariantCalling/CallVariantsONT.wdl" as VAR
 import "../../../tasks/Utility/Finalize.wdl" as FF
diff --git a/wdl/pipelines/PacBio/Alignment/PBFlowcell.wdl b/wdl/pipelines/PacBio/Alignment/PBFlowcell.wdl
index 23da6a63f..fc73ed400 100644
--- a/wdl/pipelines/PacBio/Alignment/PBFlowcell.wdl
+++ b/wdl/pipelines/PacBio/Alignment/PBFlowcell.wdl
@@ -7,10 +7,13 @@ import "../../../tasks/Preprocessing/Longbow.wdl" as Longbow
 import "../../../tasks/QC/AlignedMetrics.wdl" as AM
 import "../../../tasks/Visualization/NanoPlot.wdl" as NP
 import "../../../tasks/Utility/Finalize.wdl" as FF
-
 import "../../../tasks/Transcriptomics/MASSeq.wdl" as MAS
 
-import "../../../tasks/Utility/JupyterNotebooks.wdl" as JUPYTER
+
+struct DataTypeParameters {
+    Int num_shards
+    String map_preset
+}
 
 workflow PBFlowcell {
 
diff --git a/wdl/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl b/wdl/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl
index 84273ce53..c4a320245 100644
--- a/wdl/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl
+++ b/wdl/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl
@@ -2,7 +2,6 @@ version 1.0
 
 import "../../../tasks/Utility/PBUtils.wdl" as PB
 import "../../../tasks/Utility/Utils.wdl" as Utils
-import "../../../tasks/Alignment/AlignReads.wdl" as AR
 import "../../../tasks/Utility/Finalize.wdl" as FF
 
 workflow PBCCSIsoSeq {
diff --git a/wdl/pipelines/PacBio/Utility/PBMASIsoSeqQuantify.wdl b/wdl/pipelines/PacBio/Utility/PBMASIsoSeqQuantify.wdl
index c4050b63a..d29e94f83 100644
--- a/wdl/pipelines/PacBio/Utility/PBMASIsoSeqQuantify.wdl
+++ b/wdl/pipelines/PacBio/Utility/PBMASIsoSeqQuantify.wdl
@@ -2,10 +2,8 @@ version 1.0
 
 import "../../../tasks/Utility/Utils.wdl" as Utils
 import "../../../tasks/Utility/PBUtils.wdl" as PB
-import "../../../tasks/Alignment/AlignReads.wdl" as AR
 import "../../../tasks/Utility/StringTie2.wdl" as ST2
 import "../../../tasks/Transcriptomics/MASSeq.wdl" as MAS
-import "../../../tasks/Transcriptomics/UMI_Tools.wdl" as UMI_TOOLS
 import "../../../tasks/Transcriptomics/Preprocessing_Tasks.wdl" as TX_PRE
 import "../../../tasks/Transcriptomics/Postprocessing_Tasks.wdl" as TX_POST
 import "../../../tasks/Utility/Finalize.wdl" as FF
diff --git a/wdl/pipelines/TechAgnostic/Annotation/AnnotateTranscriptomeWithGuide.wdl b/wdl/pipelines/TechAgnostic/Annotation/AnnotateTranscriptomeWithGuide.wdl
index 14d54fa49..d6306030c 100644
--- a/wdl/pipelines/TechAgnostic/Annotation/AnnotateTranscriptomeWithGuide.wdl
+++ b/wdl/pipelines/TechAgnostic/Annotation/AnnotateTranscriptomeWithGuide.wdl
@@ -1,7 +1,5 @@
 version 1.0
 
-import "../../../tasks/Utility/PBUtils.wdl" as PB
-import "../../../tasks/Utility/Utils.wdl" as Utils
 import "../../../tasks/Utility/StringTie2.wdl"
 import "../../../tasks/Utility/Finalize.wdl" as FF
 
diff --git a/wdl/pipelines/TechAgnostic/Utility/ConvertToHailMT.wdl b/wdl/pipelines/TechAgnostic/Utility/ConvertToHailMT.wdl
index 310782a83..a0071cab7 100644
--- a/wdl/pipelines/TechAgnostic/Utility/ConvertToHailMT.wdl
+++ b/wdl/pipelines/TechAgnostic/Utility/ConvertToHailMT.wdl
@@ -1,8 +1,6 @@
 version 1.0
 
-import "../../../tasks/VariantCalling/GLNexus.wdl" as GLNexus
 import "../../../tasks/Utility/Hail.wdl" as Hail
-import "../../../tasks/Utility/Finalize.wdl" as FF
 
 workflow ConvertToHailMT {
 
diff --git a/wdl/pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl b/wdl/pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl
index fb076fdd1..f411ef583 100644
--- a/wdl/pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl
+++ b/wdl/pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl
@@ -1,5 +1,6 @@
 version 1.0
 
+import "../../../structs/Structs.wdl"
 import "../../../tasks/Utility/Utils.wdl" as Utils
 
 workflow DownloadFromSRA {
diff --git a/wdl/pipelines/TechAgnostic/Utility/DownloadFromWeb.wdl b/wdl/pipelines/TechAgnostic/Utility/DownloadFromWeb.wdl
index 7d021e562..224b26ac1 100644
--- a/wdl/pipelines/TechAgnostic/Utility/DownloadFromWeb.wdl
+++ b/wdl/pipelines/TechAgnostic/Utility/DownloadFromWeb.wdl
@@ -6,6 +6,7 @@ version 1.0
 # reimagining of the Nextflow/AWS downloading pipeline from @alaincoletta (see: http://broad.io/aws_dl).
 ##########################################################################################
 
+import "../../../structs/Structs.wdl"
 import "../../../tasks/Utility/Utils.wdl" as Utils
 
 workflow DownloadFromWeb {
diff --git a/wdl/structs/Structs.wdl b/wdl/structs/Structs.wdl
index eef96b9ce..4bed884f5 100644
--- a/wdl/structs/Structs.wdl
+++ b/wdl/structs/Structs.wdl
@@ -9,8 +9,3 @@ struct RuntimeAttr {
     Int? max_retries
     String? docker
 }
-
-struct DataTypeParameters {
-    Int num_shards
-    String map_preset
-}
diff --git a/wdl/tasks/Assembly/Hifiasm.wdl b/wdl/tasks/Assembly/Hifiasm.wdl
index 878daa73b..3f0e8bcd5 100644
--- a/wdl/tasks/Assembly/Hifiasm.wdl
+++ b/wdl/tasks/Assembly/Hifiasm.wdl
@@ -2,8 +2,6 @@ version 1.0
 
 import "../../structs/Structs.wdl"
 
-import "../Utility/Utils.wdl"
-
 workflow Hifiasm {
 
     meta {
diff --git a/wdl/tasks/Preprocessing/Guppy.wdl b/wdl/tasks/Preprocessing/Guppy.wdl
index 4ce7f51e5..7a3b57c03 100644
--- a/wdl/tasks/Preprocessing/Guppy.wdl
+++ b/wdl/tasks/Preprocessing/Guppy.wdl
@@ -9,9 +9,9 @@ version 1.0
 #   linearly but untested.
 ##########################################################################################
 
+import "../../structs/Structs.wdl"
 import "../Utility/Utils.wdl" as Utils
 import "../Utility/ONTUtils.wdl" as ONT
-import "../../structs/Structs.wdl"
 
 workflow Guppy {
 
diff --git a/wdl/tasks/Preprocessing/Longbow.wdl b/wdl/tasks/Preprocessing/Longbow.wdl
index d98561d32..f6f62283c 100644
--- a/wdl/tasks/Preprocessing/Longbow.wdl
+++ b/wdl/tasks/Preprocessing/Longbow.wdl
@@ -1,7 +1,6 @@
 version 1.0
 
 import "../../structs/Structs.wdl"
-import "../Utility/Utils.wdl"
 import "../Transcriptomics/MASSeq.wdl" as MAS
 
 struct LongbowModelParams {
diff --git a/wdl/tasks/QC/AlignedMetrics.wdl b/wdl/tasks/QC/AlignedMetrics.wdl
index 7ad2ec933..6e60abd64 100644
--- a/wdl/tasks/QC/AlignedMetrics.wdl
+++ b/wdl/tasks/QC/AlignedMetrics.wdl
@@ -1,7 +1,6 @@
 version 1.0
 
 import "../../structs/Structs.wdl"
-import "../Utility/Finalize.wdl" as FF
 
 workflow AlignedMetrics {
 
@@ -11,7 +10,7 @@ workflow AlignedMetrics {
     parameter_meta {
         aligned_bam: "Aligned BAM file"
         aligned_bai: "Index for aligned BAM file"
-        ref_fasta: "Reference FASTA file"
+        ref_fasta: "Not used"
         ref_dict: "Reference dictionary file"
         gcs_output_dir: "GCS output directory"
     }
@@ -20,13 +19,17 @@ workflow AlignedMetrics {
         File aligned_bam
         File aligned_bai
 
-        File ref_fasta
+        File? ref_fasta
         File ref_dict
 
         String? gcs_output_dir
     }
 
-    call ReadMetrics as AlignedReadMetrics { input: bam = aligned_bam }
+    call ReadMetrics {
+        input:
+            bam = aligned_bam,
+            gcs_output_dir = gcs_output_dir
+    }
 
     call MakeChrIntervalList { input: ref_dict = ref_dict }
 
@@ -35,51 +38,12 @@ workflow AlignedMetrics {
             input:
                 bam = aligned_bam,
                 bai = aligned_bai,
-                chr = chr_info[0]
-        }
-
-        call SummarizeDepth { input: regions = MosDepth.regions }
-    }
-
-    call FlagStats as AlignedFlagStats { input: bam = aligned_bam }
-
-    if (defined(gcs_output_dir)) {
-        String outdir = sub(gcs_output_dir + "", "/$", "")
-
-        call FF.FinalizeToDir as FFYieldAligned {
-            input:
-                outdir = outdir + "/yield_aligned/",
-                files = [
-                    AlignedFlagStats.flag_stats,
-                    AlignedReadMetrics.np_hist,
-                    AlignedReadMetrics.range_gap_hist,
-                    AlignedReadMetrics.zmw_hist,
-                    AlignedReadMetrics.prl_counts,
-                    AlignedReadMetrics.prl_hist,
-                    AlignedReadMetrics.prl_nx,
-                    AlignedReadMetrics.prl_yield_hist,
-                    AlignedReadMetrics.rl_counts,
-                    AlignedReadMetrics.rl_hist,
-                    AlignedReadMetrics.rl_nx,
-                    AlignedReadMetrics.rl_yield_hist
-                ]
+                chr = chr_info[0],
+                gcs_output_dir = gcs_output_dir
         }
-
-        call FF.FinalizeToDir as FFCoverageFullDist { input: outdir = outdir + "/coverage/", files = MosDepth.full_dist }
-        call FF.FinalizeToDir as FFCoverageGlobalDist { input: outdir = outdir + "/coverage/", files = MosDepth.global_dist }
-        call FF.FinalizeToDir as FFCoverageRegionDist { input: outdir = outdir + "/coverage/", files = MosDepth.region_dist }
-        call FF.FinalizeToDir as FFCoverageRegions { input: outdir = outdir + "/coverage/", files = MosDepth.regions }
-        call FF.FinalizeToDir as FFCoverageRegionsCsi { input: outdir = outdir + "/coverage/", files = MosDepth.regions_csi }
-        call FF.FinalizeToDir as FFCoverageQuantizedDist { input: outdir = outdir + "/coverage/", files = MosDepth.quantized_dist }
-        call FF.FinalizeToDir as FFCoverageQuantized { input: outdir = outdir + "/coverage/", files = MosDepth.quantized }
-        call FF.FinalizeToDir as FFCoverageQuantizedCsi { input: outdir = outdir + "/coverage/", files = MosDepth.quantized_csi }
-
-        call FF.FinalizeToDir as FFDepthSummaries { input: outdir = outdir + "/coverage_summaries/", files = SummarizeDepth.cov_summary }
     }
 
     output {
-        File aligned_flag_stats = AlignedFlagStats.flag_stats
-
         Array[File] coverage_full_dist      = MosDepth.full_dist
         Array[File] coverage_global_dist    = MosDepth.global_dist
         Array[File] coverage_region_dist    = MosDepth.region_dist
@@ -88,18 +52,20 @@ workflow AlignedMetrics {
         Array[File] coverage_quantized_dist = MosDepth.quantized_dist
         Array[File] coverage_quantized      = MosDepth.quantized
         Array[File] coverage_quantized_csi  = MosDepth.quantized_csi
-
-        File aligned_np_hist = AlignedReadMetrics.np_hist
-        File aligned_range_gap_hist = AlignedReadMetrics.range_gap_hist
-        File aligned_zmw_hist = AlignedReadMetrics.zmw_hist
-        File aligned_prl_counts = AlignedReadMetrics.prl_counts
-        File aligned_prl_hist = AlignedReadMetrics.prl_hist
-        File aligned_prl_nx = AlignedReadMetrics.prl_nx
-        File aligned_prl_yield_hist = AlignedReadMetrics.prl_yield_hist
-        File aligned_rl_counts = AlignedReadMetrics.rl_counts
-        File aligned_rl_hist = AlignedReadMetrics.rl_hist
-        File aligned_rl_nx = AlignedReadMetrics.rl_nx
-        File aligned_rl_yield_hist = AlignedReadMetrics.rl_yield_hist
+        Array[File] coverage_summary        = MosDepth.cov_summary
+
+        File aligned_np_hist = ReadMetrics.np_hist
+        File aligned_range_gap_hist = ReadMetrics.range_gap_hist
+        File aligned_zmw_hist = ReadMetrics.zmw_hist
+        File aligned_prl_counts = ReadMetrics.prl_counts
+        File aligned_prl_hist = ReadMetrics.prl_hist
+        File aligned_prl_nx = ReadMetrics.prl_nx
+        File aligned_prl_yield_hist = ReadMetrics.prl_yield_hist
+        File aligned_rl_counts = ReadMetrics.rl_counts
+        File aligned_rl_hist = ReadMetrics.rl_hist
+        File aligned_rl_nx = ReadMetrics.rl_nx
+        File aligned_rl_yield_hist = ReadMetrics.rl_yield_hist
+        File aligned_flag_stats = ReadMetrics.flag_stats
 
         File raw_chr_intervals = MakeChrIntervalList.raw_chrs
     }
@@ -133,7 +99,7 @@ task MakeChrIntervalList {
         boot_disk_gb:       10,
         preemptible_tries:  2,
         max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
+        docker:             "ubuntu:21.04"
     }
     RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
     runtime {
@@ -152,13 +118,15 @@ task MosDepth {
         File bam
         File bai
         String chr
-        Int? window_size
+        Int window_size = 500
+        String? gcs_output_dir
 
         RuntimeAttr? runtime_attr_override
     }
 
+    String? coverage_dir = if defined(gcs_output_dir) then sub(select_first([gcs_output_dir]), "/?$", "/coverage/") else gcs_output_dir
+    String? summary_dir = if defined(gcs_output_dir) then sub(select_first([gcs_output_dir]), "/?$", "/coverage_summaries/") else gcs_output_dir
     Int disk_size = 2*ceil(size(bam, "GB") + size(bai, "GB"))
-    Int ws = select_first([window_size, 500])
     String basename = basename(bam, ".bam")
     String prefix = "~{basename}.coverage.~{chr}"
 
@@ -166,7 +134,7 @@ task MosDepth {
         set -euxo pipefail
 
         mosdepth -t 4 -c "~{chr}" -n -x -Q 1 ~{prefix}.full ~{bam}
-        mosdepth -t 4 -c "~{chr}" -n -x -Q 1 -b ~{ws} ~{prefix} ~{bam}
+        mosdepth -t 4 -c "~{chr}" -n -x -Q 1 -b ~{window_size} ~{prefix} ~{bam}
 
         export MOSDEPTH_Q0=NO_COVERAGE   # 0 -- defined by the arguments to --quantize
         export MOSDEPTH_Q1=LOW_COVERAGE  # 1..4
@@ -174,6 +142,25 @@ task MosDepth {
         export MOSDEPTH_Q3=HIGH_COVERAGE # 150 ...
 
         mosdepth -t 4 -c "~{chr}" -n -x -Q 1 --quantize 0:1:5:150: ~{prefix}.quantized ~{bam}
+
+        ( echo 'chr start stop cov_mean cov_sd cov_q1 cov_median cov_q3 cov_iqr' && \
+          zcat ~{prefix}.regions.bed.gz | datamash first 1 first 2 last 3 mean 4 sstdev 4 q1 4 median 4 q3 4 iqr 4 ) | \
+            column -t > ~{prefix}.summary.txt
+
+        if ~{defined(coverage_dir)}; then
+          gsutil -m cp \
+             "~{prefix}.full.mosdepth.global.dist.txt" \
+             "~{prefix}.mosdepth.global.dist.txt" \
+             "~{prefix}.mosdepth.region.dist.txt" \
+             "~{prefix}.regions.bed.gz" \
+             "~{prefix}.regions.bed.gz.csi" \
+             "~{prefix}.quantized.mosdepth.global.dist.txt" \
+             "~{prefix}.quantized.quantized.bed.gz" \
+             "~{prefix}.quantized.quantized.bed.gz.csi" \
+             "~{coverage_dir}"
+          gsutil cp "~{prefix}.summary.txt" "~{summary_dir}"
+        fi
+
     >>>
 
     output {
@@ -185,6 +172,7 @@ task MosDepth {
         File quantized_dist = "~{prefix}.quantized.mosdepth.global.dist.txt"
         File quantized      = "~{prefix}.quantized.quantized.bed.gz"
         File quantized_csi  = "~{prefix}.quantized.quantized.bed.gz.csi"
+        File cov_summary    = "~{prefix}.summary.txt"
     }
 
     #########################
@@ -195,56 +183,7 @@ task MosDepth {
         boot_disk_gb:       10,
         preemptible_tries:  2,
         max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-mosdepth:0.3.1"
-    }
-    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])
-    }
-}
-
-task MosDepthOverBed {
-    input {
-        File bam
-        File bai
-        File bed
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    Int disk_size = 2*ceil(size(bam, "GB") + size(bai, "GB"))
-    String basename = basename(bam, ".bam")
-    String bedname = basename(bed, ".bed")
-    String prefix = "~{basename}.coverage_over_bed.~{bedname}"
-
-    command <<<
-        set -euxo pipefail
-
-        mosdepth -t 4 -b ~{bed} -n -x -Q 1 ~{prefix} ~{bam}
-    >>>
-
-    output {
-        File global_dist      = "~{prefix}.mosdepth.global.dist.txt"
-        File region_dist      = "~{prefix}.mosdepth.region.dist.txt"
-        File regions          = "~{prefix}.regions.bed.gz"
-        File regions_csi      = "~{prefix}.regions.bed.gz.csi"
-    }
-
-    #########################
-    RuntimeAttr default_attr = object {
-        cpu_cores:          4,
-        mem_gb:             8,
-        disk_gb:            disk_size,
-        boot_disk_gb:       10,
-        preemptible_tries:  2,
-        max_retries:        1,
-        docker:             "quay.io/biocontainers/mosdepth:0.2.4--he527e40_0"
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-mosdepth:0.3.2"
     }
     RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
     runtime {
@@ -258,287 +197,162 @@ task MosDepthOverBed {
     }
 }
 
-task SummarizeDepth {
-    input {
-        File regions
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    Int disk_size = 2*ceil(size(regions, "GB"))
-    String chrName = sub(basename(regions, ".regions.bed.gz"), "out.coverage.", "")
-
-    command <<<
-        set -euxo pipefail
-
-        ((echo 'chr start stop cov_mean cov_sd cov_q1 cov_median cov_q3 cov_iqr') && \
-         (zcat ~{regions} | datamash first 1 first 2 last 3 mean 4 sstdev 4 q1 4 median 4 q3 4 iqr 4)) | \
-         column -t > ~{chrName}.summary.txt
-    >>>
-
-    output {
-        File cov_summary = "~{chrName}.summary.txt"
-    }
-
-    #########################
-    RuntimeAttr default_attr = object {
-        cpu_cores:          1,
-        mem_gb:             2,
-        disk_gb:            disk_size,
-        boot_disk_gb:       10,
-        preemptible_tries:  2,
-        max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
-    }
-    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])
-    }
-}
-
-task CoverageTrack {
-    input {
-        File bam
-        File bai
-        String chr
-        String start
-        String end
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    String basename = basename(bam, ".bam")
-    Int disk_size = 2*ceil(size(bam, "GB") + size(bai, "GB"))
-
-    command <<<
-        set -euxo pipefail
-
-        samtools depth -a ~{bam} -r ~{chr}:~{start}-~{end} | bgzip > ~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz
-        tabix -p bed ~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz
-    >>>
-
-    output {
-        File coverage = "~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz"
-        File coverage_tbi = "~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz.tbi"
-    }
-
-    #########################
-    RuntimeAttr default_attr = object {
-        cpu_cores:          1,
-        mem_gb:             4,
-        disk_gb:            disk_size,
-        boot_disk_gb:       10,
-        preemptible_tries:  2,
-        max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
-    }
-    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])
-    }
-}
-
-task FlagStats {
-    input {
-        File bam
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    String basename = basename(bam, ".bam")
-    Int disk_size = 2*ceil(size(bam, "GB"))
-
-    command <<<
-        set -euxo pipefail
-
-        samtools flagstat ~{bam} > ~{basename}.flag_stats.txt
-    >>>
-
-    output {
-        File flag_stats = "~{basename}.flag_stats.txt"
-    }
-
-    #########################
-    RuntimeAttr default_attr = object {
-        cpu_cores:          1,
-        mem_gb:             4,
-        disk_gb:            disk_size,
-        boot_disk_gb:       10,
-        preemptible_tries:  2,
-        max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
-    }
-    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])
-    }
-}
-
-task ReadNamesAndLengths {
+task ReadMetrics {
     input {
         File bam
+        String? gcs_output_dir
 
         RuntimeAttr? runtime_attr_override
     }
 
+    String? output_dir = if defined(gcs_output_dir) then sub(select_first([gcs_output_dir]), "/?$", "/yield_aligned/") else gcs_output_dir
     String basename = basename(bam, ".bam")
     Int disk_size = 2*ceil(size(bam, "GB"))
 
     command <<<
         set -euxo pipefail
 
-        samtools view ~{bam} | awk '{ print $1, length($10) }' | gzip -1 > ~{basename}.read_names_and_lengths.txt.gz
-    >>>
-
-    output {
-        File read_names_and_lengths = "~{basename}.read_names_and_lengths.txt.gz"
-    }
-
-    #########################
-    RuntimeAttr default_attr = object {
-        cpu_cores:          1,
-        mem_gb:             4,
-        disk_gb:            disk_size,
-        boot_disk_gb:       10,
-        preemptible_tries:  2,
-        max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
-    }
-    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])
-    }
-}
-
-task FilterMQ0Reads {
-    input {
-        File bam
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    Int disk_size = 2*ceil(size(bam, "GB"))
-    String prefix = basename(bam, ".bam")
-
-    command <<<
-        set -euxo pipefail
-
-        samtools view -q 1 -b ~{bam} > ~{prefix}.no_mq0.bam
-        samtools index ~{prefix}.no_mq0.bam
-    >>>
-
-    output {
-        File no_mq0_bam = "~{prefix}.no_mq0.bam"
-        File no_mq0_bai = "~{prefix}.no_mq0.bam.bai"
-    }
-
-    #########################
-    RuntimeAttr default_attr = object {
-        cpu_cores:          1,
-        mem_gb:             2,
-        disk_gb:            disk_size,
-        boot_disk_gb:       10,
-        preemptible_tries:  2,
-        max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
-    }
-    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])
-    }
-}
-
-task ComputeBedCoverage {
-    input {
-        File bam
-        File bai
-        File bed
-        String prefix
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    Int disk_size = 2*ceil(size(bam, "GB") + size(bai, "GB") + size(bed, "GB"))
-
-    command <<<
-        set -euxo pipefail
-
-        bedtools coverage -b ~{bed} -a ~{bam} -nobuf | gzip > ~{prefix}.txt.gz
-        zcat ~{prefix}.txt.gz | awk '{ sum += sprintf("%f", $15*$16) } END { printf("%f\n", sum) }' > ~{prefix}.count.txt
-    >>>
-
-    output {
-        File coverage = "~{prefix}.txt.gz"
-        Float counts = read_float("~{prefix}.count.txt")
-        File counts_file = "~{prefix}.count.txt"
-    }
-
-    #########################
-    RuntimeAttr default_attr = object {
-        cpu_cores:          1,
-        mem_gb:             2,
-        disk_gb:            disk_size,
-        boot_disk_gb:       10,
-        preemptible_tries:  2,
-        max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
-    }
-    RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-    runtime {
-        cpu:                    select_first([runtime_attr.cpu_cores,         default_attr.cpu_cores])
-        memory:                 select_first([runtime_attr.mem_gb,            default_attr.mem_gb]) + " GiB"
-        disks: "local-disk " +  select_first([runtime_attr.disk_gb,           default_attr.disk_gb]) + " HDD"
-        bootDiskSizeGb:         select_first([runtime_attr.boot_disk_gb,      default_attr.boot_disk_gb])
-        preemptible:            select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-        maxRetries:             select_first([runtime_attr.max_retries,       default_attr.max_retries])
-        docker:                 select_first([runtime_attr.docker,            default_attr.docker])
-    }
-}
-
-task ReadMetrics {
-    input {
-        File bam
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    String basename = basename(bam, ".bam")
-    Int disk_size = 2*ceil(size(bam, "GB"))
+        cat << "EOF" > summarizeBAM.awk
+        BEGIN { FS=OFS="\t"; lastZMWid =-1; }
+        {
+                # retrieve the number of passes as the value of the "np" tag (default = 1)
+                nPasses=1;
+                for( fld=12;fld<=NF;++fld )
+                        if( substr($fld,1,5)=="np:i:" ) {
+                                nPasses=substr($fld,6);
+                                break;
+                        }
+
+                # get the read length and its bin for histograms
+                readLength=length($10);
+
+                # default the zero-mode waveguide id as last value + 1
+                zmwId=lastZMWid+1;
+
+                #default the range info as 0:0
+                rangeStart=0;
+                rangeStop=0;
+
+                # parse the read name
+                if( split($1,namePieces,"/")==3 ) {
+                        zmwId = namePieces[2];
+                        if( split(namePieces[3],range,"_")==2 ) {
+                                rangeStart = range[0];
+                                rangeStop = range[1];
+                        }
+                }
+
+                # calculate value to report for range gap (or -1 to indicate no report for this read)
+                reportedRangeGap=-1;
+                if( lastRangeStop!=0 && lastZMWid==zmwId ) {
+                        reportedRangeGap=rangeStart-lastRangeStop;
+                }
+
+                # calculate value to report for polymerase read length (or -1 to indicate no report for this read)
+                reportedPRL = -1;
+                if( lastZMWid!=-1 && lastZMWid!=zmwId ) {
+                        reportedPRL=polymeraseRL;
+                }
+
+                # track polymerase read length across reads with the same zmwId
+                if( zmwId!=lastZMWid ) polymeraseRL=0;
+                polymeraseRL+=readLength;
+
+                # update values maintained across reads
+                lastZMWid=zmwId;
+                lastRangeStop=rangeStop;
+
+                # print the parsed data
+                print readLength,nPasses,readLength*nPasses,zmwId,reportedRangeGap,reportedPRL;
+        }
+        EOF
+
+        cat << "EOF" > calculateNX.awk
+        BEGIN { FS=OFS="\t" }
+        {
+                sum+=$1;
+                cent=int(100.*sum/tot);
+                if( cent!=lastCent )
+                        print cent,lastVal;
+                lastCent=cent;
+                lastVal=$1
+        }
+        EOF
+
+        # awkOut.tsv file is a tab delimited file with these columns:
+        # fld:       1        2             3           4          5                      6
+        # datum: readLength nPasses yield(len*passes) zmwId reportedRangeGap reportedPolymeraseReadLength
+        samtools view -F0x900 ~{bam} | awk -f summarizeBAM.awk > awkOut.tsv
+
+        # extract the nPasses column for each read, sort numerically, count each group, add a header line
+        cut -f2 awkOut.tsv | sort -n | datamash -g1 count 1 | \
+            awk 'BEGIN{print "np\tcount"}{print}' > "~{basename}.read_metrics.np_hist.txt"
+
+        # extract the reportedRangeGap column, ignore -1 values, sort numerically, count each group, add header line
+        cut -f5 awkOut.tsv | sed '/^-1$/d' | sort -n | datamash -g1 count 1 | \
+            awk 'BEGIN{print "range_gap\tcount"}{print}' > "~{basename}.read_metrics.range_gap_hist.txt"
+
+        # extract the zmwId column, sort numerically, count each group, extract counts and sort numerically,
+        #    count each group of counts, add header line
+        cut -f4 awkOut.tsv | sort -n | datamash -g1 count 1 | cut -f2 | sort -n | datamash -g1 count 1 | \
+            awk 'BEGIN{print "zmw_count\tcount"}{print}' > "~{basename}.read_metrics.zmw_hist.txt"
+
+        # extract yield and prl, ignore -1 prls, sort numerically, mash some summary stats, add header line
+        cut -f3,6 awkOut.tsv | sed '/	-1$/d' | sort -n | datamash count 2 sum 2 sum 1 min 2 max 2 mean 2 sstdev 2 | \
+            awk 'BEGIN{print "num_polymerase_reads\tpolymerase_read_yield_bp\tpolymerase_read_yield_bp_times_passes\tpolymerase_read_min_length_bp\tpolymerase_read_max_length_bp\tpolymerase_read_mean_length_bp\tpolymerase_read_sd_length_bp"}{print}' > "~{basename}.read_metrics.prl_counts.txt"
+
+        # extract prl rounded to 100s ignoring -1 values, sort numerically, count each group, add header line
+        awk 'BEGIN{FS=OFS="\t"}{if($6>=0)print int(($6+99)/100)*100}' awkOut.tsv | sort -n | datamash -g1 count 1 | \
+            awk 'BEGIN{print "polymerase_read_length\tlength_bp"}{print}' > "~{basename}.read_metrics.prl_hist.txt"
+
+        # calculate total of prl column, ignoring -1 values
+        # then extract the prl column, ignore -1 values, reverse sort numerically, print the centile divisions,
+        #    forget about the 100th percentile, add header line
+        tot=$(cut -f6 < awkOut.tsv | sed '/^-1$/d' | datamash sum 1)
+        cut -f6 < awkOut.tsv | sed '/^-1$/d' | sort -rn | awk -v "tot=$tot" -f calculateNX.awk | sed '/^100	/d' | \
+            awk 'BEGIN{print "NX\tvalue"}{print}' > "~{basename}.read_metrics.prl_nx.txt"
+
+        # extract prl rounded to 100s and the original prl, sort numerically, sum prls for each bin, add header line
+        awk 'BEGIN{FS=OFS="\t"}{if($6>=0)print int(($6+99)/100)*100,$6}' awkOut.tsv | sort -n | datamash -g1 sum 2 | \
+            awk 'BEGIN{print "polymerase_read_length\tyield_bp"}{print}' > "~{basename}.read_metrics.prl_yield_hist.txt"
+
+        # extract readLength and yield columns, sort numerically, mash some summary stats, add header line
+        cut -f1,3 awkOut.tsv | sort -n | datamash count 1 sum 1 sum 2 min 1 max 1 mean 1 sstdev 1 | \
+            awk 'BEGIN{print "num_reads\tread_yield_bp\tread_yield_bp_times_passes\tread_min_length_bp\tread_max_length_bp\tread_mean_length_bp\tread_sd_length_bp"}{print}' > "~{basename}.read_metrics.rl_counts.txt"
+
+        # extract readLength rounded to 100s, sort numerically, count each group, add header line
+        awk 'BEGIN{FS=OFS="\t"}{print int(($1+99)/100)*100}' awkOut.tsv | sort -n | datamash -g1 count 1 | \
+            awk 'BEGIN{print "read_length_bp\tcount"}{print}' > "~{basename}.read_metrics.rl_hist.txt"
+
+        # calculate total of readLength column,
+        # then extract the readLength column, reverse sort numerically, print the centile divisions,
+        #    forget about the 100th percentile, add header line
+        tot=$(cut -f1 < awkOut.tsv | datamash sum 1)
+        cut -f1 < awkOut.tsv | sort -rn | awk -v "tot=$tot" -f calculateNX.awk | sed '/^100	/d' | \
+            awk 'BEGIN{print "NX\tvalue"}{print}' > "~{basename}.read_metrics.rl_nx.txt"
+
+        # extract readLength rounded to 100s and the original readLength, sort numerically, sum each group, add header line
+        awk 'BEGIN{FS=OFS="\t"}{print int(($1+99)/100)*100,$1}' awkOut.tsv | sort -n | datamash -g1 sum 2 | \
+            awk 'BEGIN{print "read_length\tyield_bp"}{print}' > "~{basename}.read_metrics.rl_yield_hist.txt"
 
-    command <<<
-        set -euxo pipefail
+        samtools flagstat ~{bam} > ~{basename}.flag_stats.txt
 
-        java -jar /usr/local/bin/gatk.jar ComputeLongReadMetrics -I ~{bam} -O ~{basename}.read_metrics -DF WellformedReadFilter
+        if ~{defined(output_dir)}; then
+          gsutil -m cp \
+            "~{basename}.read_metrics.np_hist.txt" \
+            "~{basename}.read_metrics.range_gap_hist.txt" \
+            "~{basename}.read_metrics.zmw_hist.txt" \
+            "~{basename}.read_metrics.prl_counts.txt" \
+            "~{basename}.read_metrics.prl_hist.txt" \
+            "~{basename}.read_metrics.prl_nx.txt" \
+            "~{basename}.read_metrics.prl_yield_hist.txt" \
+            "~{basename}.read_metrics.rl_counts.txt" \
+            "~{basename}.read_metrics.rl_hist.txt" \
+            "~{basename}.read_metrics.rl_nx.txt" \
+            "~{basename}.read_metrics.rl_yield_hist.txt" \
+            "~{basename}.flag_stats.txt" \
+            "~{output_dir}"
+        fi
     >>>
 
     output {
@@ -553,6 +367,7 @@ task ReadMetrics {
         File rl_hist = "~{basename}.read_metrics.rl_hist.txt"
         File rl_nx = "~{basename}.read_metrics.rl_nx.txt"
         File rl_yield_hist = "~{basename}.read_metrics.rl_yield_hist.txt"
+        File flag_stats = "~{basename}.flag_stats.txt"
     }
 
     #########################
@@ -563,50 +378,7 @@ task ReadMetrics {
         boot_disk_gb:       10,
         preemptible_tries:  2,
         max_retries:        1,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.11"
-    }
-    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])
-    }
-}
-
-task BamToBed {
-    input {
-        File bam
-        File bai
-
-        RuntimeAttr? runtime_attr_override
-    }
-
-    String bed = basename(bam, ".bam") + ".bed"
-    Int disk_size = 4*ceil(size(bam, "GB") + size(bai, "GB"))
-
-    command <<<
-        set -euxo pipefail
-
-        bedtools bamtobed -i ~{bam} > ~{bed}
-    >>>
-
-    output {
-        File bedfile = bed
-    }
-
-    #########################
-    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-metrics:0.1.11"
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-mini:0.1.1"
     }
     RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
     runtime {
diff --git a/wdl/tasks/QC/FPCheckAoU.wdl b/wdl/tasks/QC/FPCheckAoU.wdl
index 3c6d63107..90699a186 100644
--- a/wdl/tasks/QC/FPCheckAoU.wdl
+++ b/wdl/tasks/QC/FPCheckAoU.wdl
@@ -1,5 +1,6 @@
 version 1.0
 
+import "../../structs/Structs.wdl"
 import "../QC/Fingerprinting.wdl" as FPUtils
 import "../Utility/VariantUtils.wdl"
 
diff --git a/wdl/tasks/QC/SampleLevelAlignedMetrics.wdl b/wdl/tasks/QC/SampleLevelAlignedMetrics.wdl
index 009eb747f..2e0e595ac 100644
--- a/wdl/tasks/QC/SampleLevelAlignedMetrics.wdl
+++ b/wdl/tasks/QC/SampleLevelAlignedMetrics.wdl
@@ -1,8 +1,8 @@
 version 1.0
 
+import "../../structs/Structs.wdl"
 import "../Utility/Utils.wdl"
 import "../Visualization/NanoPlot.wdl" as NP
-import "../QC/AlignedMetrics.wdl" as AM
 
 
 workflow SampleLevelAlignedMetrics {
@@ -30,7 +30,7 @@ workflow SampleLevelAlignedMetrics {
     call NP.NanoPlotFromBam { input: bam = aligned_bam, bai = aligned_bai }
 
     if (defined(bed_to_compute_coverage)) {
-        call AM.MosDepthOverBed {
+        call MosDepthOverBed {
             input:
                 bam = aligned_bam,
                 bai = aligned_bai,
@@ -64,6 +64,55 @@ workflow SampleLevelAlignedMetrics {
     }
 }
 
+task MosDepthOverBed {
+    input {
+        File bam
+        File bai
+        File bed
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    Int disk_size = 2*ceil(size(bam, "GB") + size(bai, "GB"))
+    String basename = basename(bam, ".bam")
+    String bedname = basename(bed, ".bed")
+    String prefix = "~{basename}.coverage_over_bed.~{bedname}"
+
+    command <<<
+        set -euxo pipefail
+
+        mosdepth -t 4 -b ~{bed} -n -x -Q 1 ~{prefix} ~{bam}
+    >>>
+
+    output {
+        File global_dist      = "~{prefix}.mosdepth.global.dist.txt"
+        File region_dist      = "~{prefix}.mosdepth.region.dist.txt"
+        File regions          = "~{prefix}.regions.bed.gz"
+        File regions_csi      = "~{prefix}.regions.bed.gz.csi"
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          4,
+        mem_gb:             8,
+        disk_gb:            disk_size,
+        boot_disk_gb:       10,
+        preemptible_tries:  2,
+        max_retries:        1,
+        docker:             "quay.io/biocontainers/mosdepth:0.2.4--he527e40_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])
+    }
+}
+
 task SummarizeDepthOverWholeBed {
 
     meta {
diff --git a/wdl/tasks/VariantCalling/CallAssemblyVariants.wdl b/wdl/tasks/VariantCalling/CallAssemblyVariants.wdl
index e2c99f82b..ae5a26d69 100644
--- a/wdl/tasks/VariantCalling/CallAssemblyVariants.wdl
+++ b/wdl/tasks/VariantCalling/CallAssemblyVariants.wdl
@@ -1,7 +1,6 @@
 version 1.0
 
 import "../../structs/Structs.wdl"
-import "../Utility/Utils.wdl" as Utils
 
 workflow CallAssemblyVariants {
 
diff --git a/wdl/tasks/VariantCalling/GLNexus.wdl b/wdl/tasks/VariantCalling/GLNexus.wdl
index 966e57ed1..714492df5 100644
--- a/wdl/tasks/VariantCalling/GLNexus.wdl
+++ b/wdl/tasks/VariantCalling/GLNexus.wdl
@@ -1,7 +1,6 @@
 version 1.0
 
-import "../Utility/Utils.wdl"
-import "../Utility/VariantUtils.wdl"
+import "../../structs/Structs.wdl"
 
 workflow JointCall {