From 3fa8e18585a3451563365fb8ec1c1b256bba65c0 Mon Sep 17 00:00:00 2001 From: Mark Walker Date: Wed, 30 Aug 2023 19:52:14 -0400 Subject: [PATCH] Optimize scramble Add cores to batch wdl Update scramble git commit Update scramble wdl Fix dockerfile Fix dockerfile again Update docker Clean up wdl a bit Update scramble commit Update docker; reduce ScramblePart1 mem to 2gb Increase part2 mem to 15gib Decrease part2 mem to 12gib Optimize resources Azure docker Update scramble vcfs --- dockerfiles/scramble/Dockerfile | 71 ++++ inputs/values/dockers.json | 2 +- inputs/values/dockers_azure.json | 2 +- inputs/values/ref_panel_1kg.json | 624 ++++++++++++++--------------- wdl/GATKSVPipelineSingleSample.wdl | 6 +- wdl/GatherSampleEvidence.wdl | 13 +- wdl/GatherSampleEvidenceBatch.wdl | 10 +- wdl/Scramble.wdl | 118 ++++-- 8 files changed, 482 insertions(+), 364 deletions(-) create mode 100644 dockerfiles/scramble/Dockerfile diff --git a/dockerfiles/scramble/Dockerfile b/dockerfiles/scramble/Dockerfile new file mode 100644 index 000000000..490669d02 --- /dev/null +++ b/dockerfiles/scramble/Dockerfile @@ -0,0 +1,71 @@ +# source Image +FROM ubuntu:22.04 + +# set noninterative mode +ENV DEBIAN_FRONTEND noninteractive + +# apt-get update and install global requirements +RUN apt-get clean all && \ + apt-get update && \ + apt-get upgrade -y && \ + apt-get install -y \ + autoconf \ + autogen \ + build-essential \ + curl \ + git \ + libbz2-dev \ + libcurl4-openssl-dev \ + liblzma-dev \ + libncurses5-dev \ + libnss-sss \ + libssl-dev \ + libxml2-dev \ + ncbi-blast+ \ + r-base \ + r-bioc-biostrings \ + r-bioc-rsamtools \ + r-cran-biocmanager \ + r-cran-devtools \ + r-cran-stringr \ + r-cran-optparse \ + wget \ + zlib1g-dev + +# apt-get clean and remove cached source lists +RUN apt-get clean && \ + rm -rf /var/lib/apt/lists/* + +# install global r requirements +RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile +RUN Rscript -e "library(devtools); install_github('mhahsler/rBLAST')" + +# install bcftools and htslib +ARG HTSLIB_VERSION="1.18" +RUN mkdir -p /opt && cd /opt && \ + wget -q https://github.com/samtools/bcftools/releases/download/${HTSLIB_VERSION}/bcftools-${HTSLIB_VERSION}.tar.bz2 && \ + tar xjf bcftools-${HTSLIB_VERSION}.tar.bz2 && \ + cd bcftools-${HTSLIB_VERSION} && \ + ./configure --quiet && \ + make -s all && \ + make -s install install-htslib && \ + cd / && rm -r /opt/bcftools-${HTSLIB_VERSION} /opt/bcftools-${HTSLIB_VERSION}.tar.bz2 + +ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH + +# install scramble +ARG SCRAMBLE_COMMIT="f320d604ac030e4a7fa96b0663bcae02994c7d94" +RUN mkdir /app && cd /app \ + && git clone https://github.com/mwalker174/scramble-gatk-sv.git \ + && cd scramble-gatk-sv \ + && git checkout ${SCRAMBLE_COMMIT} \ + && cd cluster_identifier/src \ + && make \ + && ln -s /app/scramble-gatk-sv/cluster_identifier/src/build/cluster_identifier /usr/local/bin + +# test +RUN Rscript --vanilla /app/scramble-gatk-sv/cluster_analysis/bin/SCRAMble.R --help +RUN /app/scramble-gatk-sv/cluster_identifier/src/build/cluster_identifier -v + +# define default command +CMD ["Rscript"] diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json index 70267a60f..1f975369e 100644 --- a/inputs/values/dockers.json +++ b/inputs/values/dockers.json @@ -8,7 +8,7 @@ "linux_docker": "marketplace.gcr.io/google/ubuntu1804", "manta_docker": "us.gcr.io/broad-dsde-methods/vjalili/manta:5994670", "melt_docker": "us.gcr.io/talkowski-sv-gnomad/melt:3159ce1", - "scramble_docker": "us.gcr.io/broad-dsde-methods/tsharpe/scramble:1.0.2", + "scramble_docker": "us.gcr.io/broad-dsde-methods/markw/scramble:mw-scramble-99af4c50", "samtools_cloud_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2023-07-28-v0.28.1-beta-e70dfbd7", "sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2023-07-28-v0.28.1-beta-e70dfbd7", "sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/vjalili/sv-base-mini:5994670", diff --git a/inputs/values/dockers_azure.json b/inputs/values/dockers_azure.json index 845afa110..4312d1d4c 100644 --- a/inputs/values/dockers_azure.json +++ b/inputs/values/dockers_azure.json @@ -8,7 +8,7 @@ "linux_docker": "vahid.azurecr.io/google/ubuntu1804", "manta_docker": "vahid.azurecr.io/vjalili/manta:5994670", "melt_docker": "vahid.azurecr.io/melt:3159ce1", - "scramble_docker": "vahid.azurecr.io/tsharpe/scramble:1.0.2", + "scramble_docker": "vahid.azurecr.io/scramble:mw-scramble-99af4c50", "samtools_cloud_docker": "vahid.azurecr.io/gatk-sv/samtools-cloud:2023-07-28-v0.28.1-beta-e70dfbd7", "sv_base_docker": "vahid.azurecr.io/gatk-sv/sv-base:2023-07-28-v0.28.1-beta-e70dfbd7", "sv_base_mini_docker": "vahid.azurecr.io/vjalili/sv-base-mini:5994670", diff --git a/inputs/values/ref_panel_1kg.json b/inputs/values/ref_panel_1kg.json index f472a7848..d9c0657a2 100644 --- a/inputs/values/ref_panel_1kg.json +++ b/inputs/values/ref_panel_1kg.json @@ -2887,320 +2887,320 @@ ], "samples_list": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/samples_list.txt", "scramble_vcfs": [ - "gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/scramble/HG00096.scramble.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/scramble/HG00129.scramble.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/scramble/HG00140.scramble.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/scramble/HG00150.scramble.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/scramble/HG00187.scramble.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/scramble/HG00239.scramble.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/scramble/HG00277.scramble.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/scramble/HG00288.scramble.vcf.gz", - 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"sites_filtered_depth_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-FilterBatch/FilterBatch/184defa3-e61c-4757-9962-f685f6d0d204/call-FilterBatchSites/FilterBatchSites/13801c7d-9478-40dc-9a4a-2e80cbab1136/call-FilterAnnotateVcf/shard-4/cacheCopy/ref_panel_1kg.depth.with_evidence.vcf.gz", "sites_filtered_manta_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-FilterBatch/FilterBatch/184defa3-e61c-4757-9962-f685f6d0d204/call-FilterBatchSites/FilterBatchSites/13801c7d-9478-40dc-9a4a-2e80cbab1136/call-FilterAnnotateVcf/shard-0/cacheCopy/ref_panel_1kg.manta.with_evidence.vcf.gz", diff --git a/wdl/GATKSVPipelineSingleSample.wdl b/wdl/GATKSVPipelineSingleSample.wdl index ad8a73e80..2394f9930 100644 --- a/wdl/GATKSVPipelineSingleSample.wdl +++ b/wdl/GATKSVPipelineSingleSample.wdl @@ -134,7 +134,8 @@ workflow GATKSVPipelineSingleSample { RuntimeAttr? runtime_attr_melt_coverage RuntimeAttr? runtime_attr_melt_metrics RuntimeAttr? runtime_attr_melt - RuntimeAttr? runtime_attr_scramble + RuntimeAttr? runtime_attr_scramble_part1 + RuntimeAttr? runtime_attr_scramble_part2 RuntimeAttr? runtime_attr_pesr RuntimeAttr? runtime_attr_wham @@ -651,7 +652,8 @@ workflow GATKSVPipelineSingleSample { runtime_attr_melt_coverage=runtime_attr_melt_coverage, runtime_attr_melt_metrics=runtime_attr_melt_metrics, runtime_attr_melt=runtime_attr_melt, - runtime_attr_scramble=runtime_attr_scramble, + runtime_attr_scramble_part1=runtime_attr_scramble_part1, + runtime_attr_scramble_part2=runtime_attr_scramble_part2, runtime_attr_pesr=runtime_attr_pesr, runtime_attr_wham=runtime_attr_wham } diff --git a/wdl/GatherSampleEvidence.wdl b/wdl/GatherSampleEvidence.wdl index 176203a36..0c7d02624 100644 --- a/wdl/GatherSampleEvidence.wdl +++ b/wdl/GatherSampleEvidence.wdl @@ -60,6 +60,9 @@ workflow GatherSampleEvidence { Float? total_reads Int? pf_reads_improper_pairs + # Scramble inputs + Int? scramble_part2_threads + # Wham inputs File wham_include_list_bed_file @@ -95,7 +98,8 @@ workflow GatherSampleEvidence { RuntimeAttr? runtime_attr_melt_coverage RuntimeAttr? runtime_attr_melt_metrics RuntimeAttr? runtime_attr_melt - RuntimeAttr? runtime_attr_scramble + RuntimeAttr? runtime_attr_scramble_part1 + RuntimeAttr? runtime_attr_scramble_part2 RuntimeAttr? runtime_attr_pesr RuntimeAttr? runtime_attr_wham @@ -227,9 +231,12 @@ workflow GatherSampleEvidence { bam_or_cram_index = reads_index_, sample_name = sample_id, reference_fasta = reference_fasta, - detect_deletions = false, + reference_index = reference_index, + regions_list = primary_contigs_list, + part2_threads = scramble_part2_threads, scramble_docker = select_first([scramble_docker]), - runtime_attr_scramble = runtime_attr_scramble + runtime_attr_scramble_part1 = runtime_attr_scramble_part1, + runtime_attr_scramble_part2 = runtime_attr_scramble_part2 } } diff --git a/wdl/GatherSampleEvidenceBatch.wdl b/wdl/GatherSampleEvidenceBatch.wdl index 212e82736..2c5504e0b 100644 --- a/wdl/GatherSampleEvidenceBatch.wdl +++ b/wdl/GatherSampleEvidenceBatch.wdl @@ -47,6 +47,9 @@ workflow GatherSampleEvidenceBatch { Array[Float]? total_reads Array[Int]? pf_reads_improper_pairs + # Scramble inputs + Int? scramble_part2_threads + # Wham inputs File wham_include_list_bed_file @@ -80,7 +83,8 @@ workflow GatherSampleEvidenceBatch { RuntimeAttr? runtime_attr_melt_coverage RuntimeAttr? runtime_attr_melt_metrics RuntimeAttr? runtime_attr_melt - RuntimeAttr? runtime_attr_scramble + RuntimeAttr? runtime_attr_scramble_part1 + RuntimeAttr? runtime_attr_scramble_part2 RuntimeAttr? runtime_attr_pesr RuntimeAttr? runtime_attr_wham RuntimeAttr? runtime_attr_cat_metrics @@ -124,6 +128,7 @@ workflow GatherSampleEvidenceBatch { pct_chimeras = if defined(pct_chimeras) then select_first([pct_chimeras])[i] else NONE_FLOAT_, total_reads = if defined(total_reads) then select_first([total_reads])[i] else NONE_FLOAT_, pf_reads_improper_pairs = if defined(pf_reads_improper_pairs) then select_first([pf_reads_improper_pairs])[i] else NONE_INT_, + scramble_part2_threads=scramble_part2_threads, wham_include_list_bed_file = wham_include_list_bed_file, run_module_metrics = run_module_metrics_, sv_pipeline_base_docker = sv_pipeline_base_docker, @@ -147,7 +152,8 @@ workflow GatherSampleEvidenceBatch { runtime_attr_melt_coverage = runtime_attr_melt_coverage, runtime_attr_melt_metrics = runtime_attr_melt_metrics, runtime_attr_melt = runtime_attr_melt, - runtime_attr_scramble = runtime_attr_scramble, + runtime_attr_scramble_part1 = runtime_attr_scramble_part1, + runtime_attr_scramble_part2 = runtime_attr_scramble_part2, runtime_attr_pesr = runtime_attr_pesr, runtime_attr_wham = runtime_attr_wham } diff --git a/wdl/Scramble.wdl b/wdl/Scramble.wdl index 3ce73e1c9..15f6f1101 100644 --- a/wdl/Scramble.wdl +++ b/wdl/Scramble.wdl @@ -14,9 +14,12 @@ workflow Scramble { File bam_or_cram_index String sample_name File reference_fasta - Boolean detect_deletions + File reference_index + File regions_list String scramble_docker - RuntimeAttr? runtime_attr_scramble + Int? part2_threads + RuntimeAttr? runtime_attr_scramble_part1 + RuntimeAttr? runtime_attr_scramble_part2 } parameter_meta { @@ -27,41 +30,96 @@ workflow Scramble { detect_deletions: "Run deletion detection as well as mobile element insertion." } - call RunScramble { + call ScramblePart1 { input: bam_or_cram_file = bam_or_cram_file, bam_or_cram_index = bam_or_cram_index, sample_name = sample_name, + regions_list = regions_list, reference_fasta = reference_fasta, - detect_deletions = detect_deletions, + reference_index = reference_index, scramble_docker = scramble_docker, - runtime_attr_override = runtime_attr_scramble + runtime_attr_override = runtime_attr_scramble_part1 + } + + call ScramblePart2 { + input: + clusters_file = ScramblePart1.clusters_file, + sample_name = sample_name, + reference_fasta = reference_fasta, + threads = part2_threads, + scramble_docker = scramble_docker, + runtime_attr_override = runtime_attr_scramble_part2 } output { - File vcf = RunScramble.vcf - File index = RunScramble.index + File vcf = ScramblePart2.vcf + File index = ScramblePart2.index } } -task RunScramble { +task ScramblePart1 { input { File bam_or_cram_file File bam_or_cram_index String sample_name + File regions_list File reference_fasta - Boolean detect_deletions + File reference_index String scramble_docker RuntimeAttr? runtime_attr_override - File? NOT_A_FILE } - Int mem_size_gb = if detect_deletions then 16 else 3 - Int disk_size_gb = ceil(size(bam_or_cram_file,"GiB") + size(bam_or_cram_index,"GiB") + size(reference_fasta,"GiB") + 10) + Int disk_size_gb = ceil(size(bam_or_cram_file,"GiB") + size(reference_fasta,"GiB")*1.5 + 50) RuntimeAttr default_attr = object { - cpu_cores: 1, - mem_gb: mem_size_gb, + cpu_cores: 1, + mem_gb: 2.0, + disk_gb: disk_size_gb, + boot_disk_gb: 10, + preemptible_tries: 3, + max_retries: 1 + } + RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr]) + + output { + File clusters_file = "~{sample_name}.scramble_clusters.tsv.gz" + } + command <<< + set -euo pipefail + + # Identify clusters of split reads + while read region; do + time /app/scramble-gatk-sv/cluster_identifier/src/build/cluster_identifier -l -r "${region}" -t ~{reference_fasta} ~{bam_or_cram_file} \ + | gzip >> ~{sample_name}.scramble_clusters.tsv.gz + done < ~{regions_list} + >>> + 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]) + docker: scramble_docker + preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries]) + maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries]) + } +} + +task ScramblePart2 { + input { + File clusters_file + String sample_name + File reference_fasta + String scramble_docker + Int threads = 7 # Number of threads + RuntimeAttr? runtime_attr_override + } + + Int disk_size_gb = ceil(10*size(clusters_file,"GiB") + size(reference_fasta,"GiB") + 10) + + RuntimeAttr default_attr = object { + cpu_cores: 8, + mem_gb: 12.0, disk_gb: disk_size_gb, boot_disk_gb: 10, preemptible_tries: 3, @@ -78,19 +136,18 @@ task RunScramble { xDir=$PWD clusterFile=$xDir/clusters - scrambleDir="/app" + scrambleDir="/app/scramble-gatk-sv" meiRef=$scrambleDir/cluster_analysis/resources/MEI_consensus_seqs.fa # create a blast db from the reference cat ~{reference_fasta} | makeblastdb -in - -parse_seqids -title ref -dbtype nucl -out ref - # Identify clusters of split reads - $scrambleDir/cluster_identifier/src/build/cluster_identifier ~{bam_or_cram_file} > $clusterFile + gunzip -c ~{clusters_file} > $clusterFile # Produce ${clusterFile}_MEIs.txt Rscript --vanilla $scrambleDir/cluster_analysis/bin/SCRAMble.R --out-name $clusterFile \ --cluster-file $clusterFile --install-dir $scrambleDir/cluster_analysis/bin \ - --mei-refs $meiRef --ref $xDir/ref --no-vcf --eval-meis + --mei-refs $meiRef --ref $xDir/ref --no-vcf --eval-meis --cores ~{threads} # create a header for the output vcf echo \ @@ -139,31 +196,6 @@ task RunScramble { # transform the MEI descriptions into VCF lines awk -f awkScript.awk ${clusterFile}_MEIs.txt >> tmp.vcf - # work on deletions, if requested - if [ ~{detect_deletions} == "true" ] - then - # split the file of clusters to keep memory bounded - # The awk script removes lines where field 4 (the left consensus) contains nothing but 'n's - # because the deletion hunter in Scramble barfs on these. - awk '{left=$4; gsub(/n/,"",left); if ( length(left) > 0 ) print}' $clusterFile | split -a3 -l1500 - xyzzy - - # produce a xyzzy???_PredictedDeletions.txt file for each split - for fil in xyzzy??? - do Rscript --vanilla $scrambleDir/cluster_analysis/bin/SCRAMble.R --out-name $xDir/$fil \ - --cluster-file $xDir/$fil --install-dir $scrambleDir/cluster_analysis/bin \ - --mei-refs $meiRef --ref $xDir/ref --no-vcf --eval-dels - done - - # transform the *_PredictedDeletions.txt files into VCF lines, and add them to the body - awk \ - 'BEGIN{ FS=OFS="\t" } - { if(FNR<2)next - Q= $11=="NA" ? ($15=="NA"?".":$15) : ($15=="NA"?$11:($11+$15)/2) - print $1,$2+1,".","N","",Q=="."?".":int(Q),"PASS",\ - "END=" $3+1 ";SVTYPE=DEL;SVLEN=" $5 ";STRANDS=+-;CHR2=" $1 ";ALGORITHMS=scramble",\ - "GT","0/1" }' xyzzy???_PredictedDeletions.txt >> tmp.vcf - fi - # sort and index the output VCF bcftools sort -Oz "~{sample_name}.scramble.vcf.gz" bcftools index -ft "~{sample_name}.scramble.vcf.gz"