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https://github.com/MillironX/taxprofiler.git
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Make longread quality ftilering opt out
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parent
afba604e8b
commit
3f8f32cba8
4 changed files with 8 additions and 8 deletions
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@ -66,7 +66,7 @@ params {
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perform_longread_qc = false
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longread_qc_skipadaptertrim = false
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longread_qc_qualityfilter = true
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longread_qc_skipqualityfilter = true
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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_targetbases = 500000000
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@ -407,18 +407,18 @@
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"longread_qc_skipadaptertrim": {
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"type": "boolean"
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},
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"longread_qc_qualityfilter": {
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"longread_qc_skipqualityfilter": {
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"type": "boolean"
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},
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"longread_qc_qualityfilter_minlength": {
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"longread_qc_skipqualityfilter_minlength": {
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"type": "integer",
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"default": 1000
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},
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"longread_qc_qualityfilter_keeppercent": {
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"longread_qc_skipqualityfilter_keeppercent": {
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"type": "integer",
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"default": 90
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},
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"longread_qc_qualityfilter_targetbases": {
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"longread_qc_skipqualityfilter_targetbases": {
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"type": "integer",
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"default": 500000000
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},
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@ -14,7 +14,7 @@ workflow LONGREAD_PREPROCESSING {
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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if ( !params.longread_qc_skipadaptertrim && !params.longread_qc_qualityfilter ) {
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if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) {
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PORECHOP ( reads )
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ch_processed_reads = PORECHOP.out.reads
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@ -28,7 +28,7 @@ workflow LONGREAD_PREPROCESSING {
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ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
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} else if ( params.longread_qc_skipadaptertrim && params.longread_qc_qualityfilter ) {
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} else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) {
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ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
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ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
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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_qualityfilter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_skipadaptertrim false or --longread_qc_qualityfilter requested 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_skipqualityfilterrequested 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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