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adding files for CODEC pipeline #49
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f044be3
adding files for CODEC pipeline
stellaning1120 20c00d9
change fgbio version in the wdl to match on prem
stellaning1120 d585698
make eval_genome_interval/bed tunable in multiple tasks
stellaning1120 bcc80bb
add Dockerfile that buils the codec docker
stellaning1120 801bdc4
add inputs.json and modify .dockstore.yml to add 2 wdls to Dockstore
stellaning1120 110f8ac
change duplication rate calculation, add duplex efficiency calculatio…
stellaning1120 7bb7ede
add ceil() to help with disk size allocation
stellaning1120 0feeada
minor changes to task name and QC metrics collection
stellaning1120 97bcfef
minor changes to disk size input
stellaning1120 d71532f
change variant calling parameters and remove MarkDuplicated task
stellaning1120 c2347f1
change docker images since it is now public
stellaning1120 a73fe6c
not yet pushing to public
stellaning1120 ca095be
docker images chaneg to public ones
stellaning1120 21cf843
switch to public docker image
stellaning1120 dd0d44e
correct docker images
stellaning1120 852be3e
change to public docker from tag-public
stellaning1120 aaa259e
switch to public dockers
stellaning1120 e0dc64b
Add files for new module Signature Profiler of CODEC pipeline and mod…
stellaning1120 3b2f657
adding and merging pipelines for captured data
stellaning1120 60db351
adding and merging pipelines for captured data
stellaning1120 a22fb5c
Merge branch 'master' into CODEC
stellaning1120 d18b7c5
Update file fetch from task to fit GCP batch
stellaning1120 165c99a
Update file fetch from task to fit GCP batch
stellaning1120 bafa14f
update duplex efficiency calc
stellaning1120 d5079cd
minor fix to correct the read_length calc
stellaning1120 48aa1a4
set preemptibles to 0 for some time-consuming tasks
stellaning1120 db69a89
simplify the concatenate task
stellaning1120 0f915b8
correct concatenate scripts
stellaning1120 aa8a3ea
add maf2vcf function
stellaning1120 315d20c
add maf2vcf function
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| FROM --platform=linux/amd64 ubuntu:20.04 | ||
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| LABEL maintainer="lining@broadinstitute.org" | ||
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| ENV DEBIAN_FRONTEND noninteractive | ||
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| RUN apt-get update \ | ||
| && apt-get install -y software-properties-common \ | ||
| && add-apt-repository ppa:deadsnakes/ppa \ | ||
| && apt-get update \ | ||
| && apt-get install -y python3.8 python3.8-dev python3.8-venv python3-pip \ | ||
| && pip3 install pandas argparse numpy pysam | ||
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| RUN apt-get install -y r-base r-base-dev | ||
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| RUN apt-get install -y \ | ||
| git \ | ||
| wget \ | ||
| bwa \ | ||
| libssl-dev \ | ||
| g++ \ | ||
| zlib1g-dev \ | ||
| autoconf \ | ||
| libbz2-dev \ | ||
| liblzma-dev \ | ||
| libcurl4-gnutls-dev \ | ||
| libssl-dev \ | ||
| build-essential \ | ||
| software-properties-common | ||
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| RUN apt-get update -qq | ||
| RUN apt-get install -y openjdk-11-jdk | ||
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| # Clone the CODECsuite repository | ||
| RUN git clone --recursive https://github.com/broadinstitute/CODECsuite.git /CODECsuite | ||
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| RUN wget https://github.com/Kitware/CMake/releases/download/v3.28.0-rc3/cmake-3.28.0-rc3-linux-x86_64.tar.gz \ | ||
| && tar -xzvf cmake-3.28.0-rc3-linux-x86_64.tar.gz \ | ||
| && mv cmake-3.28.0-rc3-linux-x86_64 /opt/cmake-3.28 \ | ||
| && ln -s /opt/cmake-3.28/bin/cmake /usr/local/bin/cmake \ | ||
| && ln -s /opt/cmake-3.28/bin/ctest /usr/local/bin/ctest \ | ||
| && ln -s /opt/cmake-3.28/bin/cpack /usr/local/bin/cpack \ | ||
| && rm cmake-3.28.0-rc3-linux-x86_64.tar.gz | ||
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| RUN cd CODECsuite && \ | ||
| mkdir build && \ | ||
| cd build && \ | ||
| cmake .. && \ | ||
| make | ||
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| COPY dependencies/ /dependencies/ | ||
| COPY reference_files/ /reference_files/ | ||
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| RUN cp /dependencies/samtools-1.9/samtools /usr/bin/ | ||
| RUN chmod +x /CODECsuite/snakemake/script/agg_log.py | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| { | ||
| "SingleSampleCODEC.AlignMolecularConsensusReads.cpu_cores": "${2}", | ||
| "SingleSampleCODEC.AlignMolecularConsensusReads.disk_size": "${}", | ||
| "SingleSampleCODEC.AlignMolecularConsensusReads.memory": "${}", | ||
| "SingleSampleCODEC.AlignMolecularConsensusReads.threads": "${8}", | ||
| "SingleSampleCODEC.AlignRawTrimmed.disk": "${64}", | ||
| "SingleSampleCODEC.AlignRawTrimmed.disk_size": "${}", | ||
| "SingleSampleCODEC.AlignRawTrimmed.mem": "${}", | ||
| "SingleSampleCODEC.AlignRawTrimmed.memory": "${64}", | ||
| "SingleSampleCODEC.CDSByProduct.disk_size": "${}", | ||
| "SingleSampleCODEC.CDSByProduct.mem": "${}", | ||
| "SingleSampleCODEC.CSS_SFC_ErrorMetrics.disk_size": "${800}", | ||
| "SingleSampleCODEC.CSS_SFC_ErrorMetrics.memory": "${}", | ||
| "SingleSampleCODEC.CollectConsensusWgsMetrics.disk_size": "${160}", | ||
| "SingleSampleCODEC.CollectConsensusWgsMetrics.memory": "${}", | ||
| "SingleSampleCODEC.CollectInsertSizeMetrics.disk_size": "${100}", | ||
| "SingleSampleCODEC.CollectInsertSizeMetrics.memory": "${32}", | ||
| "SingleSampleCODEC.CollectRawWgsMetrics.disk_size": "${160}", | ||
| "SingleSampleCODEC.CollectRawWgsMetrics.memory": "${}", | ||
| "SingleSampleCODEC.FgbioCollapseReadFamilies.disk_size": "${200}", | ||
| "SingleSampleCODEC.FgbioCollapseReadFamilies.memory": "${}", | ||
| "SingleSampleCODEC.GroupReadByUMI.disk_size": "${400}", | ||
| "SingleSampleCODEC.GroupReadByUMI.memory": "${32}", | ||
| "SingleSampleCODEC.MarkRawDuplicates.disk_size": "${200}", | ||
| "SingleSampleCODEC.MarkRawDuplicates.memory": "${64}", | ||
| "SingleSampleCODEC.MergeAndSortMoleculeConsensusReads.disk_size": "${160}", | ||
| "SingleSampleCODEC.MergeAndSortMoleculeConsensusReads.memory": "${64}", | ||
| "SingleSampleCODEC.MergeLogSplit.disk_size": "${}", | ||
| "SingleSampleCODEC.MergeLogSplit.mem": "${}", | ||
| "SingleSampleCODEC.MergeSplit.disk_size": "${200}", | ||
| "SingleSampleCODEC.MergeSplit.memory": "${32}", | ||
| "SingleSampleCODEC.RAW_SFC_ErrorMetrics.disk_size": "${800}", | ||
| "SingleSampleCODEC.RAW_SFC_ErrorMetrics.memory": "${32}", | ||
| "SingleSampleCODEC.ReplaceRawReadGroup.disk_size": "${200}", | ||
| "SingleSampleCODEC.ReplaceRawReadGroup.memory": "${32}", | ||
| "SingleSampleCODEC.SortBam.disk_size": "${200}", | ||
| "SingleSampleCODEC.SortBam.mem": "${}", | ||
| "SingleSampleCODEC.SplitFastq1.disk_size": "${400}", | ||
| "SingleSampleCODEC.SplitFastq1.memory": "${32}", | ||
| "SingleSampleCODEC.SplitFastq2.disk_size": "${400}", | ||
| "SingleSampleCODEC.SplitFastq2.memory": "${32}", | ||
| "SingleSampleCODEC.Trim.disk_size": "${64}", | ||
| "SingleSampleCODEC.Trim.mem": "${32}", | ||
| "SingleSampleCODEC.ZipperBamAlignment.disk_size": "${200}", | ||
| "SingleSampleCODEC.ZipperBamAlignment.mem": "${32}", | ||
| "SingleSampleCODEC.eval_genome_bed": "gs://gptag/CODEC/ddbtp_codec_easy_regions.hg38.bed", | ||
| "SingleSampleCODEC.eval_genome_interval": "gs://gptag/CODEC/ddbtp_codec_easy_regions.hg38.interval_list", | ||
| "SingleSampleCODEC.fastq1": "${this.fastq1}", | ||
| "SingleSampleCODEC.fastq2": "${this.fastq2}", | ||
| "SingleSampleCODEC.germline_bam": "${this.germline_bam}", | ||
| "SingleSampleCODEC.germline_bam_index": "${this.germline_bam_index}", | ||
| "SingleSampleCODEC.num_parallel": "${40}", | ||
| "SingleSampleCODEC.reference_amb": "${workspace.referenceData_hg38_ref_amb}", | ||
| "SingleSampleCODEC.reference_ann": "${workspace.referenceData_hg38_ref_ann}", | ||
| "SingleSampleCODEC.reference_bwt": "${workspace.referenceData_hg38_ref_bwt}", | ||
| "SingleSampleCODEC.reference_dict": "${workspace.referenceData_hg38_ref_dict}", | ||
| "SingleSampleCODEC.reference_fasta": "${workspace.referenceData_hg38_ref_fasta}", | ||
| "SingleSampleCODEC.reference_fasta_index": "${workspace.referenceData_hg38_ref_fasta_index}", | ||
| "SingleSampleCODEC.reference_pac": "${workspace.referenceData_hg38_ref_pac}", | ||
| "SingleSampleCODEC.reference_sa": "${workspace.referenceData_hg38_ref_sa}", | ||
| "SingleSampleCODEC.sample_id": "${this.sample_id}", | ||
| "SingleSampleCODEC.sort_memory": "2G" | ||
| } |
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Separate CODEC Docker from the rest of Docker images that were used in the CODEC WDL.