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Make longread quality ftilering opt out

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This commit is contained in:
James Fellows Yates 2022-08-30 14:08:05 +02:00
parent afba604e8b
commit 3f8f32cba8
4 changed files with 8 additions and 8 deletions
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2
nextflow.config
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@ -66,7 +66,7 @@ params {
perform_longread_qc = false perform_longread_qc = false
longread_qc_skipadaptertrim = false longread_qc_skipadaptertrim = false
longread_qc_qualityfilter = true longread_qc_skipqualityfilter = 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

8
nextflow_schema.json
View file

@ -407,18 +407,18 @@
"longread_qc_skipadaptertrim": { "longread_qc_skipadaptertrim": {
"type": "boolean" "type": "boolean"
}, },
"longread_qc_qualityfilter": { "longread_qc_skipqualityfilter": {
"type": "boolean" "type": "boolean"
}, },
"longread_qc_qualityfilter_minlength": { "longread_qc_skipqualityfilter_minlength": {
"type": "integer", "type": "integer",
"default": 1000 "default": 1000
}, },
"longread_qc_qualityfilter_keeppercent": { "longread_qc_skipqualityfilter_keeppercent": {
"type": "integer", "type": "integer",
"default": 90 "default": 90
}, },
"longread_qc_qualityfilter_targetbases": { "longread_qc_skipqualityfilter_targetbases": {
"type": "integer", "type": "integer",
"default": 500000000 "default": 500000000
}, },

4
subworkflows/local/longread_preprocessing.nf
View file

@ -14,7 +14,7 @@ workflow LONGREAD_PREPROCESSING {
ch_versions = Channel.empty() ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty() ch_multiqc_files = Channel.empty()
if ( !params.longread_qc_skipadaptertrim && !params.longread_qc_qualityfilter ) { if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) {
PORECHOP ( reads ) PORECHOP ( reads )
ch_processed_reads = PORECHOP.out.reads ch_processed_reads = PORECHOP.out.reads
@ -28,7 +28,7 @@ workflow LONGREAD_PREPROCESSING {
ch_versions = ch_versions.mix(PORECHOP.out.versions.first()) ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log ) ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
} else if ( params.longread_qc_skipadaptertrim && params.longread_qc_qualityfilter ) { } else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) {
ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} ) ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
ch_versions = ch_versions.mix(FILTLONG.out.versions.first()) ch_versions = ch_versions.mix(FILTLONG.out.versions.first())

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_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" 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.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'"