fix(CNVkit): output

LICENSE

@@ -0,0 +1,312 @@
+Mozilla Public License Version 2.0
+
+   1. Definitions
+
+1.1. "Contributor" means each individual or legal entity that creates, contributes
+to the creation of, or owns Covered Software.
+
+1.2. "Contributor Version" means the combination of the Contributions of others
+(if any) used by a Contributor and that particular Contributor's Contribution.
+
+      1.3. "Contribution" means Covered Software of a particular Contributor.
+
+1.4. "Covered Software" means Source Code Form to which the initial Contributor
+has attached the notice in Exhibit A, the Executable Form of such Source Code
+Form, and Modifications of such Source Code Form, in each case including portions
+thereof.
+
+      1.5. "Incompatible With Secondary Licenses" means
+
+(a) that the initial Contributor has attached the notice described in Exhibit
+B to the Covered Software; or
+
+(b) that the Covered Software was made available under the terms of version
+1.1 or earlier of the License, but not also under the terms of a Secondary
+License.
+
+1.6. "Executable Form" means any form of the work other than Source Code Form.
+
+1.7. "Larger Work" means a work that combines Covered Software with other
+material, in a separate file or files, that is not Covered Software.
+
+      1.8. "License" means this document.
+
+1.9. "Licensable" means having the right to grant, to the maximum extent possible,
+whether at the time of the initial grant or subsequently, any and all of the
+rights conveyed by this License.
+
+      1.10. "Modifications" means any of the following:
+
+(a) any file in Source Code Form that results from an addition to, deletion
+from, or modification of the contents of Covered Software; or
+
+(b) any new file in Source Code Form that contains any Covered Software.
+
+1.11. "Patent Claims" of a Contributor means any patent claim(s), including
+without limitation, method, process, and apparatus claims, in any patent Licensable
+by such Contributor that would be infringed, but for the grant of the License,
+by the making, using, selling, offering for sale, having made, import, or
+transfer of either its Contributions or its Contributor Version.
+
+1.12. "Secondary License" means either the GNU General Public License, Version
+2.0, the GNU Lesser General Public License, Version 2.1, the GNU Affero General
+Public License, Version 3.0, or any later versions of those licenses.
+
+1.13. "Source Code Form" means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your") means an individual or a legal entity exercising rights
+under this License. For legal entities, "You" includes any entity that controls,
+is controlled by, or is under common control with You. For purposes of this
+definition, "control" means (a) the power, direct or indirect, to cause the
+direction or management of such entity, whether by contract or otherwise,
+or (b) ownership of more than fifty percent (50%) of the outstanding shares
+or beneficial ownership of such entity.
+
+   2. License Grants and Conditions
+
+      2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free, non-exclusive
+license:
+
+(a) under intellectual property rights (other than patent or trademark) Licensable
+by such Contributor to use, reproduce, make available, modify, display, perform,
+distribute, and otherwise exploit its Contributions, either on an unmodified
+basis, with Modifications, or as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer for
+sale, have made, import, and otherwise transfer either its Contributions or
+its Contributor Version.
+
+      2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution become
+effective for each Contribution on the date the Contributor first distributes
+such Contribution.
+
+      2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under this
+License. No additional rights or licenses will be implied from the distribution
+or licensing of Covered Software under this License. Notwithstanding Section
+2.1(b) above, no patent license is granted by a Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software; or
+
+(b) for infringements caused by: (i) Your and any other third party's modifications
+of Covered Software, or (ii) the combination of its Contributions with other
+software (except as part of its Contributor Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of its
+Contributions.
+
+This License does not grant any rights in the trademarks, service marks, or
+logos of any Contributor (except as may be necessary to comply with the notice
+requirements in Section 3.4).
+
+      2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to distribute
+the Covered Software under a subsequent version of this License (see Section
+10.2) or under the terms of a Secondary License (if permitted under the terms
+of Section 3.3).
+
+      2.5. Representation
+
+Each Contributor represents that the Contributor believes its Contributions
+are its original creation(s) or it has sufficient rights to grant the rights
+to its Contributions conveyed by this License.
+
+      2.6. Fair Use
+
+This License is not intended to limit any rights You have under applicable
+copyright doctrines of fair use, fair dealing, or other equivalents.
+
+      2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted in
+Section 2.1.
+
+   3. Responsibilities
+
+      3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any Modifications
+that You create or to which You contribute, must be under the terms of this
+License. You must inform recipients that the Source Code Form of the Covered
+Software is governed by the terms of this License, and how they can obtain
+a copy of this License. You may not attempt to alter or restrict the recipients'
+rights in the Source Code Form.
+
+      3.2. Distribution of Executable Form
+
+      If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code Form,
+as described in Section 3.1, and You must inform recipients of the Executable
+Form how they can obtain a copy of such Source Code Form by reasonable means
+in a timely manner, at a charge no more than the cost of distribution to the
+recipient; and
+
+(b) You may distribute such Executable Form under the terms of this License,
+or sublicense it under different terms, provided that the license for the
+Executable Form does not attempt to limit or alter the recipients' rights
+in the Source Code Form under this License.
+
+      3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice, provided
+that You also comply with the requirements of this License for the Covered
+Software. If the Larger Work is a combination of Covered Software with a work
+governed by one or more Secondary Licenses, and the Covered Software is not
+Incompatible With Secondary Licenses, this License permits You to additionally
+distribute such Covered Software under the terms of such Secondary License(s),
+so that the recipient of the Larger Work may, at their option, further distribute
+the Covered Software under the terms of either this License or such Secondary
+License(s).
+
+      3.4. Notices
+
+You may not remove or alter the substance of any license notices (including
+copyright notices, patent notices, disclaimers of warranty, or limitations
+of liability) contained within the Source Code Form of the Covered Software,
+except that You may alter any license notices to the extent required to remedy
+known factual inaccuracies.
+
+      3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support, indemnity
+or liability obligations to one or more recipients of Covered Software. However,
+You may do so only on Your own behalf, and not on behalf of any Contributor.
+You must make it absolutely clear that any such warranty, support, indemnity,
+or liability obligation is offered by You alone, and You hereby agree to indemnify
+every Contributor for any liability incurred by such Contributor as a result
+of warranty, support, indemnity or liability terms You offer. You may include
+additional disclaimers of warranty and limitations of liability specific to
+any jurisdiction.
+
+   4. Inability to Comply Due to Statute or Regulation
+
+If it is impossible for You to comply with any of the terms of this License
+with respect to some or all of the Covered Software due to statute, judicial
+order, or regulation then You must: (a) comply with the terms of this License
+to the maximum extent possible; and (b) describe the limitations and the code
+they affect. Such description must be placed in a text file included with
+all distributions of the Covered Software under this License. Except to the
+extent prohibited by statute or regulation, such description must be sufficiently
+detailed for a recipient of ordinary skill to be able to understand it.
+
+   5. Termination
+
+5.1. The rights granted under this License will terminate automatically if
+You fail to comply with any of its terms. However, if You become compliant,
+then the rights granted under this License from a particular Contributor are
+reinstated (a) provisionally, unless and until such Contributor explicitly
+and finally terminates Your grants, and (b) on an ongoing basis, if such Contributor
+fails to notify You of the non-compliance by some reasonable means prior to
+60 days after You have come back into compliance. Moreover, Your grants from
+a particular Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the first
+time You have received notice of non-compliance with this License from such
+Contributor, and You become compliant prior to 30 days after Your receipt
+of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent infringement
+claim (excluding declaratory judgment actions, counter-claims, and cross-claims)
+alleging that a Contributor Version directly or indirectly infringes any patent,
+then the rights granted to You by any and all Contributors for the Covered
+Software under Section 2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all end
+user license agreements (excluding distributors and resellers) which have
+been validly granted by You or Your distributors under this License prior
+to termination shall survive termination.
+
+   6. Disclaimer of Warranty
+
+Covered Software is provided under this License on an "as is" basis, without
+warranty of any kind, either expressed, implied, or statutory, including,
+without limitation, warranties that the Covered Software is free of defects,
+merchantable, fit for a particular purpose or non-infringing. The entire risk
+as to the quality and performance of the Covered Software is with You. Should
+any Covered Software prove defective in any respect, You (not any Contributor)
+assume the cost of any necessary servicing, repair, or correction. This disclaimer
+of warranty constitutes an essential part of this License. No use of any Covered
+Software is authorized under this License except under this disclaimer.
+
+   7. Limitation of Liability
+
+Under no circumstances and under no legal theory, whether tort (including
+negligence), contract, or otherwise, shall any Contributor, or anyone who
+distributes Covered Software as permitted above, be liable to You for any
+direct, indirect, special, incidental, or consequential damages of any character
+including, without limitation, damages for lost profits, loss of goodwill,
+work stoppage, computer failure or malfunction, or any and all other commercial
+damages or losses, even if such party shall have been informed of the possibility
+of such damages. This limitation of liability shall not apply to liability
+for death or personal injury resulting from such party's negligence to the
+extent applicable law prohibits such limitation. Some jurisdictions do not
+allow the exclusion or limitation of incidental or consequential damages,
+so this exclusion and limitation may not apply to You.
+
+   8. Litigation
+
+Any litigation relating to this License may be brought only in the courts
+of a jurisdiction where the defendant maintains its principal place of business
+and such litigation shall be governed by laws of that jurisdiction, without
+reference to its conflict-of-law provisions. Nothing in this Section shall
+prevent a party's ability to bring cross-claims or counter-claims.
+
+   9. Miscellaneous
+
+This License represents the complete agreement concerning the subject matter
+hereof. If any provision of this License is held to be unenforceable, such
+provision shall be reformed only to the extent necessary to make it enforceable.
+Any law or regulation which provides that the language of a contract shall
+be construed against the drafter shall not be used to construe this License
+against a Contributor.
+
+   10. Versions of the License
+
+      10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section 10.3,
+no one other than the license steward has the right to modify or publish new
+versions of this License. Each version will be given a distinguishing version
+number.
+
+      10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version of
+the License under which You originally received the Covered Software, or under
+the terms of any subsequent version published by the license steward.
+
+      10.3. Modified Versions
+
+If you create software not governed by this License, and you want to create
+a new license for such software, you may create and use a modified version
+of this License if you rename the license and remove any references to the
+name of the license steward (except to note that such modified license differs
+from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With Secondary
+Licenses under the terms of this version of the License, the notice described
+in Exhibit B of this License must be attached. Exhibit A - Source Code Form
+License Notice
+
+This Source Code Form is subject to the terms of the Mozilla Public License,
+v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain
+one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular file,
+then You may include the notice in a location (such as a LICENSE file in a
+relevant directory) where a recipient would be likely to look for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+
+This Source Code Form is "Incompatible With Secondary Licenses", as defined
+by the Mozilla Public License, v. 2.0.

README.md

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+# poi-upstream
+
+Automated integrated analysis software for genomics data of the cancer patients.

defaults

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+{
+  "tumor_bam": "",
+  "tumor_bam_index": "",
+  "normal_bam": "",
+  "normal_bam_index": "",
+  "read_structure": "",
+  "duplex_umi": "",
+  "platform": "MGI",
+  "regions": "oss://ivd-product/reference/bed/Dynegene/SureSelectXT_HS_V8_S33266340_hg38_Regions.bed",
+  "interval_padding": "0",
+  "SENTIEON_LICENSE": "172.25.164.226:8990",
+  "fasta": "GRCh38_full_analysis_set_plus_decoy_hla.fa",
+  "ref_dir": "oss://ivd-product/reference/refGenome/",
+  "ref_flat": "oss://ivd-product/reference/refGenome/refFlat.hg38.txt",
+  "dbmills_dir": "oss://genomics-platform-reference-data/GRCh38.d1.vd1/",
+  "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
+  "dbsnp": "dbsnp_146.hg38.vcf",
+  "dbsnp_dir": "oss://genomics-platform-reference-data/GRCh38.d1.vd1/",
+  "annovar_database": "oss://genomics-platform-reference-data/annovar/",
+  "annotsv_database": "oss://ivd-product/reference/AnnotSV/",
+  "germline_resource": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",
+  "germline_resource_tbi": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
+  "gc": "oss://ivd-product/reference/Sequenza/GRCh38.gc50Base.wig.gz",
+  "baseline": "oss://ivd-product/reference/MSIsensor/hg38_reference.list_baseline",
+  "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sentieon-genomics:v202112.05",
+  "manta_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/manta:1.6.0",
+  "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/bcftools:v1.9",
+  "annovar_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annovar:v20191024",
+  "annotsv_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annotsv:3.1.3",
+  "cnvkit_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/cnvkit:0.9.8",
+  "sequenza_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sequenza:3.0.0",
+  "msisensor_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/msisensor-pro:1.2.0",
+  "tmb_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/tmb:1.0.0",
+  "cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "disk_size": "200"
+}

inputs

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+{
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.hrd": "{{ hrd }}",
+  "{{ project_name }}.tumor_bam": "{{ tumor_bam }}",
+  "{{ project_name }}.tumor_bam_index": "{{ tumor_bam_index }}",
+  "{{ project_name }}.normal_bam": "{{ normal_bam }}",
+  "{{ project_name }}.normal_bam_index": "{{ normal_bam_index }}",
+  "{{ project_name }}.read_structure": "{{ read_structure }}",
+  "{{ project_name }}.duplex_umi": "{{ duplex_umi }}",
+  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
+  "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
+  "{{ project_name }}.manta_docker": "{{ manta_docker }}",
+  "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
+  "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
+  "{{ project_name }}.annotsv_docker": "{{ annotsv_docker }}",
+  "{{ project_name }}.cnvkit_docker": "{{ cnvkit_docker }}",
+  "{{ project_name }}.sequenza_docker": "{{ sequenza_docker }}",
+  "{{ project_name }}.msisensor_docker": "{{ msisensor_docker }}",
+  "{{ project_name }}.tmb_docker": "{{ tmb_docker }}",
+  "{{ project_name }}.platform": "{{ platform }}",
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}",
+  "{{ project_name }}.dbsnp": "{{ dbsnp }}",
+  "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
+  "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
+  "{{ project_name }}.db_mills": "{{ db_mills }}",
+  "{{ project_name }}.germline_resource": "{{ germline_resource }}",
+  "{{ project_name }}.germline_resource_tbi": "{{ germline_resource_tbi }}",
+  "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.interval_padding": "{{ interval_padding }}",
+  "{{ project_name }}.annovar_database": "{{ annovar_database }}",
+  "{{ project_name }}.annotsv_database": "{{ annotsv_database }}",
+  "{{ project_name }}.gc": "{{ gc }}",
+  "{{ project_name }}.baseline": "{{ baseline }}",
+  "{{ project_name }}.ref_flat": "{{ ref_flat }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/ANNOVAR.wdl

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+task ANNOVAR {
+
+  File vcf
+  String basename = basename(vcf,".vcf")
+  File annovar_database
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    /installations/annovar/table_annovar.pl ${vcf} \
+    ${annovar_database} -buildver hg38 \
+    -out ${basename} -remove \
+    -protocol refGene,cytoBand,genomicSuperDups,clinvar_20220320,intervar_20180118,cosmic95_coding,cosmic95_noncoding,gnomad211_exome,dbnsfp42c,avsnp150 \
+    -operation g,r,r,f,f,f,f,f,f,f \
+    -nastring . -vcfinput -polish -thread $nt
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File avinput = "${basename}.avinput"
+    File multianno_txt = "${basename}.hg38_multianno.txt"
+    File multianno_vcf = "${basename}.hg38_multianno.vcf"
+  }
+}

tasks/AnnotSV.wdl

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+task AnnotSV {
+  
+  String sample
+  File somatic_vcf
+  File? germline_vcf
+  File annotsv_database
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    export ANNOTSV=/opt/AnnotSV
+    if [ ${somatic_vcf} ]; then
+      $ANNOTSV/bin/AnnotSV -SVinputFile ${somatic_vcf} -outputFile ${sample}.somatic.SV.annotated.tsv -genomeBuild GRCh38 -annotationsDir ${annotsv_database} -outputDir .
+    fi
+    if [ ${germline_vcf} ]; then
+      $ANNOTSV/bin/AnnotSV -SVinputFile ${germline_vcf} -outputFile ${sample}.germline.SV.annotated.tsv -genomeBuild GRCh38 -annotationsDir ${annotsv_database} -outputDir .
+    fi
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File AnnotSV_somatic_SV = "${sample}.somatic.SV.annotated.tsv"
+    File? AnnotSV_germline_SV = "${sample}.germline.SV.annotated.tsv"
+  }
+}

tasks/BQSR.wdl

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+task BQSR {
+  
+  File ref_dir
+  File dbsnp_dir
+  File dbmills_dir
+  
+  String sample
+  String SENTIEON_LICENSE
+  String fasta
+  String dbsnp
+  String db_mills
+  File deduped_bam
+  File deduped_bam_index
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+
+    sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} -i ${deduped_bam} \
+    --algo QualCal \
+    -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
+    ${sample}_recal_data.table
+
+    sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} -i ${deduped_bam} -q ${sample}_recal_data.table \
+    --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
+    ${sample}_recal_data.table.post --algo ReadWriter ${sample}.sorted.deduped.recaled.bam
+
+    sentieon driver -t $nt --algo QualCal \
+    --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
+
+    sentieon plot bqsr -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File recal_table = "${sample}_recal_data.table"
+    File recal_post = "${sample}_recal_data.table.post"
+    File recaled_bam = "${sample}.sorted.deduped.recaled.bam"
+    File recaled_bam_index = "${sample}.sorted.deduped.recaled.bam.bai"
+    File recal_csv = "${sample}_recal_data.csv"
+    File bqsrreport_pdf = "${sample}_bqsrreport.pdf"
+  }
+}

tasks/CNVkit.wdl

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+task CNVkit {
+  
+  String sample
+  File ref_dir
+  String fasta
+  File ref_flat
+  File regions
+  File hrd
+  File tumor_bam
+  File tumor_bam_index
+  File? normal_bam
+  File? normal_bam_index
+  String docker
+  String cluster_config
+  String disk_size
+  
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    cnvkit.py access ${ref_dir}/${fasta} -o access.bed
+    # Prepare the target bed
+    cnvkit.py target ${regions} --annotate ${ref_flat} --split --short-names -o my_baits.bed
+    if [ ${normal_bam} ]; then
+      cnvkit.py autobin ${tumor_bam} ${normal_bam} -t my_baits.bed -g access.bed
+    else
+      cnvkit.py autobin ${tumor_bam} -t my_baits.bed -g access.bed
+    fi
+    
+    # For each sample...
+    cnvkit.py coverage ${tumor_bam} my_baits.target.bed -o ${sample}.T.targetcoverage.cnn
+    cnvkit.py coverage ${tumor_bam} my_baits.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn
+    if [ ${normal_bam} ]; then
+      cnvkit.py coverage ${normal_bam} my_baits.target.bed -o ${sample}.N.targetcoverage.cnn
+      cnvkit.py coverage ${normal_bam} my_baits.antitarget.bed -o ${sample}.N.antitargetcoverage.cnn
+      # With paired or pooled normals
+      cnvkit.py reference *.N.{,anti}targetcoverage.cnn --fasta ${ref_dir}/${fasta} -o reference.cnn
+    else
+      # With no control sample
+      cnvkit.py reference -o reference.cnn -f ${ref_dir}/${fasta} -t my_baits.target.bed -a my_baits.antitarget.bed
+    fi
+    
+    # For each tumor sample...
+    cnvkit.py fix ${sample}.T.targetcoverage.cnn ${sample}.T.antitargetcoverage.cnn reference.cnn -o ${sample}.cnr
+    cnvkit.py segment ${sample}.cnr -o ${sample}.cns
+    
+    # Check noise
+    cnvkit.py metrics ${sample}.cnr -s ${sample}.cns > ${sample}.stats
+    
+    # Derive each segment's absolute integer copy number, ploidy must be int value
+    PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
+    cnvkit.py call ${sample}.cns -y -m clonal --purity $PURITY -o ${sample}.call.cns
+    cnvkit.py call ${sample}.cnr -y -m clonal --purity $PURITY -o ${sample}.call.cnr
+
+    # Plot the results
+    cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf
+    cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
+    cnvkit.py heatmap ${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
+    
+    # Genemetrics
+    mkdir gainloss
+    cnvkit.py genemetrics ${sample}.call.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
+    cnvkit.py genemetrics ${sample}.call.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt
+    # Filter genes
+    cat ${sample}.ratio_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > ratio_cnv.txt
+    cat ${sample}.segment_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > segment_cnv.txt
+    comm -12 ratio_cnv.txt segment_cnv.txt > ${sample}.trusted_genes.txt
+    for gene in `cat ${sample}.trusted_genes.txt`
+    do
+      cnvkit.py scatter ${sample}.call.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf
+    done
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File scatter_pdf = "${sample}.scatter.pdf"
+    File diagram_pdf = "${sample}.diagram.pdf"
+    File heatmap_pdf = "${sample}.heatmap.pdf"
+    File cnr = "${sample}.cnr"
+    File cns = "${sample}.cns"
+    File stats = "${sample}.stats"
+    File call_cnr = "${sample}.call.cnr"
+    File call_cns = "${sample}.call.cns"
+    File ratio_cnv = "${sample}.ratio_cnv.txt"
+    File segment_cnv = "${sample}.segment_cnv.txt"
+    File gainloss_genes = "${sample}.trusted_genes.txt"
+    Array[File] gainloss = glob("./gainloss/*")
+  }
+}

tasks/Dedup.wdl

@@ -0,0 +1,34 @@
+task Dedup {
+  
+  String SENTIEON_LICENSE
+  String sample
+
+  File sorted_bam
+  File sorted_bam_index
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    sentieon driver -t $nt -i ${sorted_bam} --algo LocusCollector --fun score_info ${sample}_score.txt
+    sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File score = "${sample}_score.txt"
+    File dedup_metrics = "${sample}_dedup_metrics.txt"
+    File deduped_bam = "${sample}.sorted.deduped.bam"
+    File deduped_bam_index = "${sample}.sorted.deduped.bam.bai"
+  }
+}

tasks/HRD.wdl

@@ -0,0 +1,67 @@
+task HRD {
+  
+  String sample
+  File ref_dir
+  String fasta
+  File gc
+  File tumor_bam
+  File tumor_bam_index
+  File? normal_bam
+  File? normal_bam_index
+  String docker
+  String cluster_config
+  String disk_size
+  
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    seqz=${sample}'.seqz.gz'
+    small=${sample}'.small.seqz.gz'
+    
+    # bam2seqz
+    sequenza-utils bam2seqz -gc ${gc} --fasta ${ref_dir}/${fasta} -n ${normal_bam} -t ${tumor_bam} -o $seqz -C chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY --parallel 24
+    
+    # merge and remove
+    zcat ${sample}_*.seqz.gz | awk '{if (NR == 1 || (NR != 1 && $1 != "chromosome")) {print $0}}' | bgzip > $seqz
+    tabix -f -s 1 -b 2 -e 2 -S 1 $seqz
+    rm ${sample}_*.seqz.gz; rm ${sample}_*.seqz.gz.tbi
+    
+    # seqz_binning: WES: 50; WGS: 200
+    sequenza-utils seqz_binning --seqz $seqz -w 50 -o $small
+    
+    # analysis in r
+    Rscript /home/sequenza/sequenza.r '.' ${sample}
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File hrd="${sample}.HRD.txt"
+    File alternative_fit="${sample}_alternative_fit.pdf"
+    File alternative_solutions="${sample}_alternative_solutions.txt"
+    File chromosome_depths="${sample}_chromosome_depths.pdf"
+    File chromosome_view="${sample}_chromosome_view.pdf"
+    File CN_bars="${sample}_CN_bars.pdf"
+    File confints_CP="${sample}_confints_CP.txt"
+    File contours_CP="${sample}_contours_CP.pdf"
+    File CP_contours="${sample}_CP_contours.pdf"
+    File gc_plots="${sample}_gc_plots.pdf"
+    File genome_view="${sample}_genome_view.pdf"
+    File model_fit="${sample}_model_fit.pdf"
+    File mutations="${sample}_mutations.txt"
+    File scarHRD_input="${sample}_scarHRD_input.txt"
+    File segments="${sample}_segments.txt"
+    File sequenza_cp_table="${sample}_sequenza_cp_table.RData"
+    File sequenza_extract="${sample}_sequenza_extract.RData"
+    File sequenza_log="${sample}_sequenza_log.txt"
+    File small_seqz="${sample}.small.seqz.gz"
+    File small_seqz_index="${sample}.small.seqz.gz.tbi"
+  }
+}

tasks/Haplotyper.wdl

@@ -0,0 +1,51 @@
+task Haplotyper {
+  
+  File ref_dir
+  String fasta
+  File dbsnp_dir
+  
+  String SENTIEON_LICENSE
+  File recaled_bam
+  File recaled_bam_index
+  String dbsnp
+  String sample
+  String docker
+  String cluster_config
+  String disk_size
+  
+  File? regions
+  Int? interval_padding
+  
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+    else
+      INTERVAL=""
+    fi
+
+    sentieon driver -t $nt \
+    --interval ${regions} -r ${ref_dir}/${fasta} \
+    -i ${recaled_bam} \
+    --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} \
+    ${sample}.Haplotyper.vcf
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File vcf = "${sample}.Haplotyper.vcf"
+    File vcf_idx = "${sample}.Haplotyper.vcf.idx"
+  }
+}
+
+

tasks/MSIsensor.wdl

@@ -0,0 +1,41 @@
+task MSIsensor {
+  
+  String sample
+  File ref_dir
+  String fasta
+  File tumor_bam
+  File tumor_bam_index
+  File? normal_bam
+  File? normal_bam_index
+  File baseline
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    # MSI
+		mkdir -p /cromwell_root/tmp/
+    msisensor-pro scan -d ${ref_dir}/${fasta} -o reference.list
+    if [ ${normal_bam} ]; then
+      msisensor-pro msi -d reference.list -n ${normal_bam} -t ${tumor_bam} -o /cromwell_root/tmp/${sample}
+    else
+      msisensor-pro pro -d ${baseline} -t ${tumor_bam} -o /cromwell_root/tmp/${sample}
+    fi
+    cp /cromwell_root/tmp/${sample} ${sample}.MSI.txt
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File msi = "${sample}.MSI.txt"
+  }
+}

tasks/Manta.wdl

@@ -0,0 +1,61 @@
+task Manta {
+  
+  File ref_dir
+	File fasta
+  File regions
+  File tumor_bam
+  File tumor_bam_index
+  File? normal_bam
+  File? normal_bam_index
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+  
+	command <<<
+    set -o pipefail
+    set -e
+		nt=$(nproc)
+    
+    MANTA_INSTALL_PATH="/opt/manta-1.6.0.centos6_x86_64"
+    MANTA_ANALYSIS_PATH="/cromwell_root/tmp"
+		mkdir -p $MANTA_ANALYSIS_PATH
+    
+    cp ${regions} my_baits.bed
+    bgzip -c my_baits.bed > my_baits.bed.gz
+    tabix -p bed my_baits.bed.gz
+    # input files
+    if [ ${normal_bam} ]; then
+      INPUT="--normalBam ${normal_bam} --tumorBam ${tumor_bam}"
+    else
+      INPUT="--tumorBam ${tumor_bam}"
+    fi
+    # configManta
+    $MANTA_INSTALL_PATH/bin/configManta.py \
+    $INPUT \
+    --callRegions my_baits.bed.gz --exome \
+    --referenceFasta ${ref_dir}/${fasta} \
+    --runDir $MANTA_ANALYSIS_PATH
+    # runWorkflow
+    $MANTA_ANALYSIS_PATH/runWorkflow.py -j $nt
+    # results
+    if [ ${normal_bam} ]; then
+      cp $MANTA_ANALYSIS_PATH/results/variants/somaticSV.vcf.gz ${sample}.Manta.somaticSV.vcf.gz
+      cp $MANTA_ANALYSIS_PATH/results/variants/diploidSV.vcf.gz ${sample}.Manta.germlineSV.vcf.gz
+    else
+      cp $MANTA_ANALYSIS_PATH/results/variants/tumorSV.vcf.gz ${sample}.Manta.somaticSV.vcf.gz
+    fi
+	>>>
+  
+	runtime {
+		docker:docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+  
+	output {
+		File somatic_vcf = "${sample}.Manta.somaticSV.vcf.gz"
+		File? germline_vcf = "${sample}.Manta.germlineSV.vcf.gz"
+	}
+}

tasks/Metrics.wdl

@@ -0,0 +1,69 @@
+task Metrics {
+
+  File ref_dir
+  String SENTIEON_LICENSE
+  String sample
+  String docker
+  String cluster_config
+
+  String fasta
+  File sorted_bam
+  File sorted_bam_index
+  String disk_size
+
+  File? regions
+
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions}"
+    else
+      INTERVAL=""
+    fi
+    
+    sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} $INTERVAL \
+    -i ${sorted_bam} \
+    --algo CoverageMetrics --omit_base_output ${sample}_coverage_metrics \
+    --algo MeanQualityByCycle ${sample}_mq_metrics.txt \
+    --algo QualDistribution ${sample}_qd_metrics.txt \
+    --algo GCBias --summary ${sample}_gc_summary.txt ${sample}_gc_metrics.txt \
+    --algo AlignmentStat ${sample}_aln_metrics.txt \
+    --algo InsertSizeMetricAlgo ${sample}_is_metrics.txt \
+    --algo QualityYield ${sample}_QualityYield.txt \
+    --algo WgsMetricsAlgo ${sample}_WgsMetricsAlgo.txt
+    
+    sentieon plot metrics -o ${sample}_metrics_report.pdf gc=${sample}_gc_metrics.txt qd=${sample}_qd_metrics.txt mq=${sample}_mq_metrics.txt isize=${sample}_is_metrics.txt
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File coverage_metrics_sample_summary = "${sample}_coverage_metrics.sample_summary"
+    File coverage_metrics_sample_statistics = "${sample}_coverage_metrics.sample_statistics"
+    File coverage_metrics_sample_interval_statistics = "${sample}_coverage_metrics.sample_interval_statistics"
+    File coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_coverage_metrics.sample_cumulative_coverage_proportions"
+    File coverage_metrics_sample_cumulative_coverage_counts = "${sample}_coverage_metrics.sample_cumulative_coverage_counts"
+    File qd_metrics = "${sample}_qd_metrics.txt"
+    File mq_metrics = "${sample}_mq_metrics.txt"
+    File is_metrics = "${sample}_is_metrics.txt"
+    File gc_summary = "${sample}_gc_summary.txt"
+    File gc_metrics = "${sample}_gc_metrics.txt"
+    File aln_metrics = "${sample}_aln_metrics.txt"
+    File QualityYield = "${sample}_QualityYield.txt"
+    File wgsmetrics = "${sample}_WgsMetricsAlgo.txt"
+    File qd_metrics_pdf = "${sample}_qd_metrics.pdf"
+    File mq_metrics_pdf = "${sample}_mq_metrics.pdf"
+    File is_metrics_pdf = "${sample}_is_metrics.pdf"
+    File gc_metrics_pdf = "${sample}_gc_metrics.pdf"
+  }
+}

tasks/TMB.wdl

@@ -0,0 +1,33 @@
+task TMB {
+  
+  String sample
+  File regions
+  File snpindel_txt
+  String docker
+  String cluster_config
+  String disk_size
+  
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    sort -k1,1 -k2,2n ${regions} | bedtools merge -i - > merged.bed
+    size=`awk -F'\t' 'BEGIN{SUM=0}{SUM+=$3-$2}END{print SUM}' merged.bed`
+    
+    # analysis in python
+    python ~/tmb.py ${snpindel_txt} $size ${sample}
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File snp_indel="${sample}.snp_indel.txt"
+    File tmb="${sample}.TMB.txt"
+  }
+}

tasks/TNseq.wdl

@@ -0,0 +1,79 @@
+task TNseq {
+  
+  String sample
+  String SENTIEON_LICENSE
+  File tumor_bam
+  File tumor_bam_index
+  File? normal_bam
+  File? normal_bam_index
+  String tumor_name
+  String normal_name
+  
+  File ref_dir
+  String fasta
+  File germline_resource
+  File germline_resource_tbi
+  File? regions
+  Int? interval_padding
+  
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+    else
+      INTERVAL=""
+    fi
+    
+    if [ ${normal_bam} ]; then
+      INPUT="-i ${tumor_bam} -i ${normal_bam}"
+      SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}"
+    else
+      INPUT="-i ${tumor_bam}"
+      SAMPLE="--tumor_sample ${tumor_name}"
+    fi
+    
+    sentieon driver -t $nt -r ${ref_dir}/${fasta} \
+    $INPUT $INTERVAL \
+    --algo TNhaplotyper2 $SAMPLE \
+    --germline_vcf ${germline_resource} \
+    ${sample}.TNseq.raw.vcf \
+    --algo OrientationBias --tumor_sample ${tumor_name} \
+    ${sample}.orientation \
+    --algo ContaminationModel $SAMPLE \
+    --vcf ${germline_resource} \
+    --tumor_segments ${sample}.contamination.segments \
+    ${sample}.contamination
+    
+    sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} \
+    --algo TNfilter $SAMPLE \
+    -v ${sample}.TNseq.raw.vcf \
+    --contamination ${sample}.contamination \
+    --tumor_segments ${sample}.contamination.segments \
+    --orientation_priors ${sample}.orientation \
+    ${sample}.TNseq.vcf
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File vcf = "${sample}.TNseq.vcf"
+    File vcf_index = "${sample}.TNseq.vcf.idx"
+    File contamination = "${sample}.contamination"
+    File contamination_segments = "${sample}.contamination.segments"
+    File orientation = "${sample}.orientation"
+  }
+}

tasks/bcftools.wdl

@@ -0,0 +1,29 @@
+task bcftools {
+  
+  File ref_dir
+  String fasta
+  File vcf
+  String basename = basename(vcf,".vcf")
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    bcftools norm -m -both ${vcf} | bcftools norm -f ${ref_dir}/${fasta} -Ov -o ${basename}.norm.vcf
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File norm_vcf = "${basename}.norm.vcf"
+  }
+}

tasks/deduped_Metrics.wdl

@@ -0,0 +1,62 @@
+task deduped_Metrics {
+
+  File ref_dir
+  String SENTIEON_LICENSE
+  String sample
+  String fasta
+  File deduped_bam
+  File deduped_bam_index
+  String docker
+  String cluster_config
+  String disk_size
+  
+  File? regions
+
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions}"
+    else
+      INTERVAL=""
+    fi
+
+    sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} $INTERVAL \
+    -i ${deduped_bam} \
+    --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics \
+    --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt \
+    --algo QualDistribution ${sample}_deduped_qd_metrics.txt \
+    --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt \
+    --algo AlignmentStat ${sample}_deduped_aln_metrics.txt \
+    --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt \
+    --algo QualityYield ${sample}_deduped_QualityYield.txt \
+    --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo.txt
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File deduped_coverage_metrics_sample_summary = "${sample}_deduped_coverage_metrics.sample_summary"
+    File deduped_coverage_metrics_sample_statistics = "${sample}_deduped_coverage_metrics.sample_statistics"
+    File deduped_coverage_metrics_sample_interval_statistics = "${sample}_deduped_coverage_metrics.sample_interval_statistics"
+    File deduped_coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_proportions"
+    File deduped_coverage_metrics_sample_cumulative_coverage_counts = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_counts"
+    File deduped_mean_quality = "${sample}_deduped_mq_metrics.txt"
+    File deduped_qd_metrics = "${sample}_deduped_qd_metrics.txt"
+    File deduped_gc_summary = "${sample}_deduped_gc_summary.txt"
+    File deduped_gc_metrics = "${sample}_deduped_gc_metrics.txt"
+    File dedeuped_aln_metrics = "${sample}_deduped_aln_metrics.txt"
+    File deduped_is_metrics = "${sample}_deduped_is_metrics.txt"
+    File deduped_QualityYield = "${sample}_deduped_QualityYield.txt"
+    File deduped_wgsmetrics = "${sample}_deduped_WgsMetricsAlgo.txt"
+  }
+}

tasks/mapping.wdl

@@ -0,0 +1,52 @@
+task mapping {
+
+  File ref_dir
+  String fasta
+  File fastq_1
+  File fastq_2
+  
+  String SENTIEON_LICENSE
+  String group
+  String sample
+  String platform
+  String? duplex_umi
+  String? read_structure
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    
+    if [ ${read_structure} ]; then
+      if [ ${duplex_umi} == "true" ]; then
+        READ_STRUCTURE="-d ${read_structure}"
+      fi
+      sentieon umi extract $READ_STRUCTURE ${fastq_1} ${fastq_2} | \
+      sentieon bwa mem -p -C -R "@RG\tID:${group}\tSM:${sample}\tPL:${platform}" -t $nt -K 10000000 ${ref_dir}/${fasta} - | \
+      sentieon umi consensus -o ${sample}.umi_consensus.fastq.gz
+      
+      sentieon bwa mem -p -C -R "@RG\tID:${group}\tSM:${sample}\tPL:${platform}" -t $nt -K 10000000 $fasta ${sample}.umi_consensus.fastq.gz | \
+      sentieon util sort --umi_post_process --sam2bam -i - -o ${sample}.sorted.bam
+    else
+      sentieon bwa mem -R "@RG\tID:${group}\tSM:${sample}\tPL:${platform}" \
+      -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | \
+      sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
+    fi
+    
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File sorted_bam = "${sample}.sorted.bam"
+    File sorted_bam_index = "${sample}.sorted.bam.bai"
+  }
+}

workflow.wdl

@@ -0,0 +1,71 @@
+import "./tasks/Haplotyper.wdl" as Haplotyper
+import "./tasks/TNseq.wdl" as TNseq
+import "./tasks/bcftools.wdl" as bcftools
+import "./tasks/ANNOVAR.wdl" as ANNOVAR
+import "./tasks/Manta.wdl" as Manta
+import "./tasks/AnnotSV.wdl" as AnnotSV
+import "./tasks/CNVkit.wdl" as CNVkit
+import "./tasks/MSIsensor.wdl" as MSIsensor
+import "./tasks/HRD.wdl" as HRD
+import "./tasks/TMB.wdl" as TMB
+
+workflow {{ project_name }} {
+  
+  String sample_id
+  File hrd
+  File? tumor_bam
+  File? tumor_bam_index
+  File? normal_bam
+  File? normal_bam_index
+  String? duplex_umi
+  String? read_structure
+  
+  String SENTIEON_LICENSE
+  String sentieon_docker
+  String manta_docker
+  String bcftools_docker
+  String annovar_docker
+  String annotsv_docker
+  String cnvkit_docker
+  String sequenza_docker
+  String msisensor_docker
+  String tmb_docker
+  
+  String platform
+  File ref_dir
+  String fasta
+  File dbmills_dir
+  String db_mills
+  File dbsnp_dir
+  String dbsnp
+  File germline_resource
+  File germline_resource_tbi
+  File annovar_database
+  File annotsv_database
+  File gc
+  File baseline
+  File ref_flat
+  
+  File? regions
+  Int? interval_padding
+  
+  String disk_size
+  String cluster_config
+  
+  call CNVkit.CNVkit as CNVkit {
+    input:
+    sample=sample_id,
+    fasta=fasta,
+    ref_dir=ref_dir,
+    regions=regions,
+    ref_flat=ref_flat,
+    normal_bam=normal_bam,
+    normal_bam_index=normal_bam_index,
+    tumor_bam=tumor_bam,
+    tumor_bam_index=tumor_bam_index,
+    hrd=hrd,
+    docker=cnvkit_docker,
+    cluster_config=cluster_config,
+    disk_size=disk_size
+  }
+}