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a little cleanup #422
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a little cleanup #422
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934f1ca
a little cleanup
tedsharpe b622439
improved AlignedMetrics
tedsharpe d324901
get rid of weird gatk version in ReadMetrics task
tedsharpe 6ab28a2
fix missing Structs import in scrapbook
tedsharpe 3b8b9f5
delete test json for now
tedsharpe 9674dd2
dammit
tedsharpe ceaf133
bump mosdepth version
tedsharpe f9dc53a
remove MergeVCFs.wdl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -5,6 +5,7 @@ channels: | |
| - bioconda | ||
| - r | ||
| dependencies: | ||
| - conda-forge::ncurses | ||
| - samtools | ||
| - bedtools | ||
| - java-jdk | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| FROM us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2023-07-28-v0.28.1-beta-e70dfbd7 | ||
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| #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/??_* | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| IMAGE_NAME = lr-mini | ||
| VERSION = 0.1.1 | ||
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||
| TAG1 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):$(VERSION) | ||
| TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):latest | ||
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| all: | build push | ||
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| build: | ||
| docker build -t $(TAG1) -t $(TAG2) . | ||
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| build_no_cache: | ||
| docker build --no-cache -t $(TAG1) -t $(TAG2) . | ||
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| push: | ||
| docker push $(TAG1) | ||
| docker push $(TAG2) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,185 @@ | ||
| version 1.0 | ||
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|
||
| import "../../structs/Structs.wdl" | ||
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| task CoverageTrack { | ||
| input { | ||
| File bam | ||
| File bai | ||
| String chr | ||
| String start | ||
| String end | ||
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| RuntimeAttr? runtime_attr_override | ||
| } | ||
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| String basename = basename(bam, ".bam") | ||
| Int disk_size = 2*ceil(size(bam, "GB") + size(bai, "GB")) | ||
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| command <<< | ||
| set -euxo pipefail | ||
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| 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 | ||
| >>> | ||
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| output { | ||
| File coverage = "~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz" | ||
| File coverage_tbi = "~{basename}.coverage.~{chr}_~{start}_~{end}.txt.gz.tbi" | ||
| } | ||
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||
| ######################### | ||
| 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]) | ||
| } | ||
| } | ||
|
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||
| task FilterMQ0Reads { | ||
| input { | ||
| File bam | ||
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| RuntimeAttr? runtime_attr_override | ||
| } | ||
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| Int disk_size = 2*ceil(size(bam, "GB")) | ||
| String prefix = basename(bam, ".bam") | ||
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| command <<< | ||
| set -euxo pipefail | ||
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| samtools view -q 1 -b ~{bam} > ~{prefix}.no_mq0.bam | ||
| samtools index ~{prefix}.no_mq0.bam | ||
| >>> | ||
|
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||
| output { | ||
| File no_mq0_bam = "~{prefix}.no_mq0.bam" | ||
| File no_mq0_bai = "~{prefix}.no_mq0.bam.bai" | ||
| } | ||
|
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||
| ######################### | ||
| 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]) | ||
| } | ||
| } | ||
|
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||
| task ComputeBedCoverage { | ||
| input { | ||
| File bam | ||
| File bai | ||
| File bed | ||
| String prefix | ||
|
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||
| RuntimeAttr? runtime_attr_override | ||
| } | ||
|
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| Int disk_size = 2*ceil(size(bam, "GB") + size(bai, "GB") + size(bed, "GB")) | ||
|
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| command <<< | ||
| set -euxo pipefail | ||
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| 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 | ||
| >>> | ||
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| output { | ||
| File coverage = "~{prefix}.txt.gz" | ||
| Float counts = read_float("~{prefix}.count.txt") | ||
| File counts_file = "~{prefix}.count.txt" | ||
| } | ||
|
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| ######################### | ||
| 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]) | ||
| } | ||
| } | ||
|
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| task BamToBed { | ||
| input { | ||
| File bam | ||
| File bai | ||
|
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| RuntimeAttr? runtime_attr_override | ||
| } | ||
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| String bed = basename(bam, ".bam") + ".bed" | ||
| Int disk_size = 4*ceil(size(bam, "GB") + size(bai, "GB")) | ||
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| command <<< | ||
| set -euxo pipefail | ||
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| bedtools bamtobed -i ~{bam} > ~{bed} | ||
| >>> | ||
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| output { | ||
| File bedfile = bed | ||
| } | ||
|
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| ######################### | ||
| 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]) | ||
| } | ||
| } |
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2 changes: 0 additions & 2 deletions
2
wdl/pipelines/TechAgnostic/Annotation/AnnotateTranscriptomeWithGuide.wdl
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I know we have
0.3.2on GCR, but given that themainbranch is using0.3.1, we can do one of two things here:0.3.2changed from0.3.1. I see you included several more packages inlr-mosdepth, so if you built that, then let's also bump the version in the makefile in that docker foler.There was a problem hiding this comment.
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Makefile version bumped.