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Fix accidental overly zelous search-and-replace
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2 changed files with 4 additions and 4 deletions
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@ -410,15 +410,15 @@
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"longread_qc_skipqualityfilter": {
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"type": "boolean"
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},
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"longread_qc_skipqualityfilter_minlength": {
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"longread_qc_qualityfilter_minlength": {
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"type": "integer",
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"default": 1000
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},
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"longread_qc_skipqualityfilter_keeppercent": {
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"longread_qc_qualityfilter_keeppercent": {
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"type": "integer",
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"default": 90
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},
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"longread_qc_skipqualityfilter_targetbases": {
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"longread_qc_qualityfilter_targetbases": {
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"type": "integer",
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"default": 500000000
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},
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@ -22,7 +22,7 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
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if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_qc_excludeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_qc_mergepairs"
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if ( (!params.longread_qc_skipadaptertrim || !params.longread_qc_skipqualityfilter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_skipadaptertrim false or --longread_qc_skipqualityfilterrequested but quality-control not turned on. Please specify --perform_long_qc"
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if ( (!params.longread_qc_skipadaptertrim || !params.longread_qc_skipqualityfilter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_skipadaptertrim false or --longread_qc_skipqualityfilter requested but quality-control not turned on. Please specify --perform_long_qc"
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if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' )) exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"
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