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Fix accidental overly zelous search-and-replace

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James Fellows Yates 2022-08-30 14:11:48 +02:00
parent 3f8f32cba8
commit 8917e29e35
2 changed files with 4 additions and 4 deletions
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6
nextflow_schema.json
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@ -410,15 +410,15 @@
"longread_qc_skipqualityfilter": { "longread_qc_skipqualityfilter": {
"type": "boolean" "type": "boolean"
}, },
"longread_qc_skipqualityfilter_minlength": { "longread_qc_qualityfilter_minlength": {
"type": "integer", "type": "integer",
"default": 1000 "default": 1000
}, },
"longread_qc_skipqualityfilter_keeppercent": { "longread_qc_qualityfilter_keeppercent": {
"type": "integer", "type": "integer",
"default": 90 "default": 90
}, },
"longread_qc_skipqualityfilter_targetbases": { "longread_qc_qualityfilter_targetbases": {
"type": "integer", "type": "integer",
"default": 500000000 "default": 500000000
}, },

2
workflows/taxprofiler.nf
View file

@ -22,7 +22,7 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
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." 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."
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" 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"
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" 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"
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'" 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'"