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Make everything within opt-out, once QC is opted-in
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parent
95ad380173
commit
afba604e8b
3 changed files with 3 additions and 7 deletions
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@ -27,8 +27,6 @@ params {
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perform_shortread_qc = true
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perform_shortread_qc = true
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perform_longread_qc = true
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perform_longread_qc = true
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shortread_qc_mergepairs = true
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shortread_qc_mergepairs = true
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longread_qc_skipadaptertrim = false
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longread_qc_qualityfilter = true
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perform_shortread_complexityfilter = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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perform_longread_hostremoval = true
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@ -27,8 +27,6 @@ params {
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perform_shortread_qc = true
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perform_shortread_qc = true
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perform_longread_qc = true
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perform_longread_qc = true
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shortread_qc_mergepairs = true
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shortread_qc_mergepairs = true
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longread_qc_skipadaptertrim = false
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longread_qc_qualityfilter = true
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perform_shortread_complexityfilter = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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perform_longread_hostremoval = true
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@ -58,15 +58,15 @@ params {
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perform_shortread_qc = false
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perform_shortread_qc = false
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shortread_qc_tool = 'fastp'
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shortread_qc_tool = 'fastp'
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shortread_qc_skipadaptertrim = false
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shortread_qc_skipadaptertrim = false
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shortread_qc_mergepairs = false
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shortread_qc_mergepairs = true
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shortread_qc_excludeunmerged = false
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shortread_qc_excludeunmerged = false
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shortread_qc_adapter1 = null
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shortread_qc_adapter1 = null
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shortread_qc_adapter2 = null
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shortread_qc_adapter2 = null
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shortread_qc_minlength = 0
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shortread_qc_minlength = 15
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perform_longread_qc = false
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perform_longread_qc = false
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longread_qc_skipadaptertrim = false
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longread_qc_skipadaptertrim = false
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longread_qc_qualityfilter = false
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longread_qc_qualityfilter = true
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longread_qc_qualityfilter_minlength = 1000
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longread_qc_qualityfilter_minlength = 1000
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longread_qc_qualityfilter_keeppercent = 90
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longread_qc_qualityfilter_keeppercent = 90
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longread_qc_qualityfilter_targetbases = 500000000
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longread_qc_qualityfilter_targetbases = 500000000
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