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Make everything within opt-out, once QC is opted-in

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This commit is contained in:
James Fellows Yates 2022-08-30 14:04:34 +02:00
parent 95ad380173
commit afba604e8b
3 changed files with 3 additions and 7 deletions
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2
conf/test.config
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@ -27,8 +27,6 @@ params {
perform_shortread_qc = true perform_shortread_qc = true
perform_longread_qc = true perform_longread_qc = true
shortread_qc_mergepairs = true shortread_qc_mergepairs = true
longread_qc_skipadaptertrim = false
longread_qc_qualityfilter = true
perform_shortread_complexityfilter = true perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true perform_shortread_hostremoval = true
perform_longread_hostremoval = true perform_longread_hostremoval = true

2
conf/test_noprofiling.config
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@ -27,8 +27,6 @@ params {
perform_shortread_qc = true perform_shortread_qc = true
perform_longread_qc = true perform_longread_qc = true
shortread_qc_mergepairs = true shortread_qc_mergepairs = true
longread_qc_skipadaptertrim = false
longread_qc_qualityfilter = true
perform_shortread_complexityfilter = true perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true perform_shortread_hostremoval = true
perform_longread_hostremoval = true perform_longread_hostremoval = true

6
nextflow.config
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@ -58,15 +58,15 @@ params {
perform_shortread_qc = false perform_shortread_qc = false
shortread_qc_tool = 'fastp' shortread_qc_tool = 'fastp'
shortread_qc_skipadaptertrim = false shortread_qc_skipadaptertrim = false
shortread_qc_mergepairs = false shortread_qc_mergepairs = true
shortread_qc_excludeunmerged = false shortread_qc_excludeunmerged = false
shortread_qc_adapter1 = null shortread_qc_adapter1 = null
shortread_qc_adapter2 = null shortread_qc_adapter2 = null
shortread_qc_minlength = 0 shortread_qc_minlength = 15
perform_longread_qc = false perform_longread_qc = false
longread_qc_skipadaptertrim = false longread_qc_skipadaptertrim = false
longread_qc_qualityfilter = false longread_qc_qualityfilter = true
longread_qc_qualityfilter_minlength = 1000 longread_qc_qualityfilter_minlength = 1000
longread_qc_qualityfilter_keeppercent = 90 longread_qc_qualityfilter_keeppercent = 90
longread_qc_qualityfilter_targetbases = 500000000 longread_qc_qualityfilter_targetbases = 500000000