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merge metadata changes and updated raw imports from develop to master (#91)
* Add metadata to workflows published on dockstore (#89) * add metadata to u_of_michigan_aligner.wdl * add metadata to FunctionalEquivalence.wdl * add metadata for topmed_freeze3_calling.wdl * add metadata sbg-alignment-cwl/topmed-alignment.cwl * add metadata functional equivalent aligner: /topmed-cwl/workflow/alignment_workflow.cwl * add metadata to topmed_freeze3_calling.cwl * add metadata topmed_variant_calling_pipeline.cwl * update raw imports for 1.32.0 release (#90)
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‎CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.wdl‎

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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/CRAM-no-header-md5sum/md5sum/CRAM_md5sum.wdl" as f1
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/CRAM-no-header-md5sum/checker/CRAM_md5sum_checker.wdl" as f2
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/CRAM-no-header-md5sum/md5sum/CRAM_md5sum.wdl" as f1
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/CRAM-no-header-md5sum/checker/CRAM_md5sum_checker.wdl" as f2
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workflow CRAMMd5sumChecker {
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File inputCRAMFile

‎aligner/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl‎

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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/aligner/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/aligner/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/aligner/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/aligner/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker
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workflow checkerWorkflow {
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Int expectedNumofReads

‎aligner/functional-equivalence-wdl/FunctionalEquivalence.wdl‎

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File output_cram_index = ConvertToCram.output_cram_index
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File output_cram_md5 = ConvertToCram.output_cram_md5
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}
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meta {
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author : "Ruchi Munshi"
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email : "rmunshi@broadinstitute.org"
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description: "A WDL workflow based on the [CCDG pipeline standards](https://github.com/CCDG/Pipeline-Standardization/blob/master/PipelineStandard.md) for processing high-throughput sequencing data."
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}
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}
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# TASK DEFINITIONS

‎aligner/sbg-alignment-cwl/topmed-alignment.cwl‎

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doc: >-
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A CWL wrapper of the TopMed alignment workflow described here:
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https://github.com/statgen/docker-alignment
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Tool Author: Hyun Min Kang (hmkang@umich.edu) and Adrian Tan (atks@umich.edu)
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Wrapper Author: Marko Zecevic (marko.zecevic@sbgenomics.com)
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label: TOPMed Alignment
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$namespaces:
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sbg: 'https://sevenbridges.com'

‎aligner/topmed-cwl/workflow/alignment_workflow.cwl‎

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- reads are provided in query-sorted order
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- all reads must have an RG tag
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- Reference genome must be Hg38 with ALT contigs
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'dct:creator':
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'foaf:mbox': 'mailto:yilinxu@uchicago.edu'
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'foaf:name': Yilin Xu
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class: Workflow
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id: alignment_pipeline

‎aligner/u_of_michigan_aligner-checker/u_of_michigan_aligner_checker.wdl‎

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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/aligner/u_of_michigan_aligner/u_of_michigan_aligner.wdl" as TopMed_aligner
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/aligner/u_of_michigan_aligner-checker/u_of_michigan_aligner_checker_calculation.wdl" as checker
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/aligner/u_of_michigan_aligner/u_of_michigan_aligner.wdl" as TopMed_aligner
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/aligner/u_of_michigan_aligner-checker/u_of_michigan_aligner_checker_calculation.wdl" as checker
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workflow checkerWorkflow {
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String docker_image

‎aligner/u_of_michigan_aligner/u_of_michigan_aligner.wdl‎

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File aligner_output_cram = PostAlign.output_cram_file
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File aligner_output_crai = PostAlign.output_crai_file
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}
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meta {
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author : "Walt Shands"
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email : "jshands@ucsc.edu"
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description: "This is the workflow WDL for the [TOPMed/University of Michigan alignment pipeline](https://github.com/statgen/docker-alignment)"
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}
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}
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task PreAlign {

‎variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl‎

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cwlVersion: v1.0
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id: >-
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vladimir_obucina/topmed-freeze-3a-variant-calling-pipeline/topmed_freeze3_calling/25
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doc: >-
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This is the CWL wrapper for U of Michigan's [TOPMed Freeze 3a Variant Calling Pipeline](https://github.com/statgen/topmed_freeze3_calling)
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baseCommand: []
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inputs:
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- format: 'BAI,CRAI'
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'sbg:projectName': TOPMed Freeze 3a Variant Calling Pipeline
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'sbg:createdBy': mikojicic
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'sbg:modifiedBy': vladimir_obucina
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'dct:creator':
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'foaf:mbox': 'mailto:vladimir.obucina@sbgenomics.com'
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'foaf:name': Vladimir Obucina
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'sbg:validationErrors': []

‎variant-caller/sbg-variant-caller-cwl/topmed_variant_calling_pipeline.cwl‎

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cwlVersion: v1.0
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id: >-
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vladimir_obucina/topmed-freeze-3a-variant-calling-pipeline/topmed-variant-calling-pipeline-cwl1/17
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doc: >-
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This is the CWL wrapper for U of Michigan's [TOPMed Freeze 3a Variant Calling Pipeline](https://github.com/statgen/topmed_freeze3_calling)
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label: TOPMed Variant Calling Pipeline CWL1
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inputs:
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- id: reference
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- class: InlineJavascriptRequirement
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$namespaces:
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sbg: 'https://sevenbridges.com'
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'dct:creator':
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'foaf:mbox': 'mailto:vladimir.obucina@sbgenomics.com'
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'foaf:name': Vladimir Obucina
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‎variant-caller/variant-caller-wdl-checker/topmed_freeze3_calling_checker.wdl‎

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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/variant-caller/variant-caller-wdl/topmed_freeze3_calling.wdl" as TopMed_variantcaller
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/variant-caller/variant-caller-wdl-checker/topmed-variantcaller-checker.wdl" as checker
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/variant-caller/variant-caller-wdl/topmed_freeze3_calling.wdl" as TopMed_variantcaller
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import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/variant-caller/variant-caller-wdl-checker/topmed-variantcaller-checker.wdl" as checker
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workflow checkerWorkflow {
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File inputTruthVCFFile

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