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profiles {
  standard {
    includeConfig 'nextflowConf/biohpc.config'
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  }
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  biohpc {
    includeConfig 'nextflowConf/biohpc.config'
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  }
  biohpc_max {
    includeConfig 'nextflowConf/biohpc_max.config'
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  }
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  dnanexus {
    includeConfig 'nextflowConf/dnanexus.config'
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  aws {
    includeConfig 'nextflowConf/aws.config'
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  }
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process {
  withName:trackStart {
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    container = 'gudmaprbk/gudmap-rbk_base:1.0.1'
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  withName:getBag {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
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  }
  withName:getData {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
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    container = 'gudmaprbk/python3:1.0.1'
  withName:getRefERCC {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
  }
  withName:getRef {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
  }
  withName:fastqc {
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    container = 'gudmaprbk/fastqc0.11.9:1.0.1'
  withName:seqwho {
    container = 'gudmaprbk/seqwho1.0.0:1.0.0'
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    container = 'gudmaprbk/trimgalore0.6.6:1.0.0'
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    container = 'gudmaprbk/seqtk1.3:1.0.1'
  withName:alignSampleDataERCC {
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    container = 'gudmaprbk/hisat2.2.1:1.0.1'
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    container = 'gudmaprbk/hisat2.2.1:1.0.1'
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    container = 'gudmaprbk/rseqc4.0.0:1.0.1'
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    container = 'gudmaprbk/gudmap-rbk_base:1.0.1'
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    container = 'gudmaprbk/hisat2.2.1:1.0.1'
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    container = 'gudmaprbk/picard2.25.0:1.0.0'
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    container = 'gudmaprbk/subread2.0.1:1.0.1'
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    container = 'gudmaprbk/deeptools3.5.0:1.0.1'
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    container = 'gudmaprbk/rseqc4.0.0:1.0.1'
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    container = 'gudmaprbk/multiqc1.10:1.0.0'
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  withName:uploadInputBag {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
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  }
  withName:uploadExecutionRun {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
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  withName:uploadQC {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
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  }
  withName:uploadProcessedFile {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
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  }
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  withName:uploadOutputBag {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
  withName:finalizeExecutionRun {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
  withName:failPreExecutionRun {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
  withName:failPreExecutionRun_seqwho {
    container = 'gudmaprbk/deriva1.4:1.0.1'
  }
  withName:failExecutionRun {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
  withName:uploadQC_fail {
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    container = 'gudmaprbk/deriva1.4:1.0.1'
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  accessToken = '3eyJ0aWQiOiAzODIyfS42YWFjOWMwZDM4Mjc1NmY0MGJiY2QxNWRkOTZlYTU4MDlmY2NkZmRj'
  workspaceId = '84512216752206'
  enabled = true
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}
  name = 'gudmap_rbk/rna-seq'
  homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
  description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.'
  mainScript = 'rna-seq.nf'
  version = 'v2.0.0'
  nextflowVersion = '>=20.01.0'