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Merge pull request #113 from nf-core/filtlong-in-tests

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Improve longread QC parameters
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James A. Fellows Yates 2022-08-31 09:36:12 +02:00 committed by GitHub
commit 394084a31b
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7 changed files with 19 additions and 18 deletions
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6
conf/modules.config
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@ -136,9 +136,9 @@ process {
withName: FILTLONG { withName: FILTLONG {
ext.args = [ ext.args = [
"--min_length ${params.longread_qc_minlength}", "--min_length ${params.longread_qc_qualityfilter_minlength}",
"--keep_percent ${params.longread_qc_keep_percent}", "--keep_percent ${params.longread_qc_qualityfilter_keeppercent}",
"--target_bases ${params.longread_qc_target_bases}" "--target_bases ${params.longread_qc_qualityfilter_targetbases}"
] ]
.join(' ').trim() .join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" } ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }

1
conf/test.config
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@ -26,6 +26,7 @@ params {
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv' databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_qc = true perform_shortread_qc = true
perform_longread_qc = true perform_longread_qc = true
shortread_qc_mergepairs = 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

1
conf/test_noprofiling.config
View file

@ -26,6 +26,7 @@ params {
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv' databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_qc = true perform_shortread_qc = true
perform_longread_qc = true perform_longread_qc = true
shortread_qc_mergepairs = 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

12
nextflow.config
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@ -58,18 +58,18 @@ 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 = 15 shortread_qc_minlength = 15
perform_longread_qc = false perform_longread_qc = false
longread_qc_run_clip = false longread_qc_skipadaptertrim = false
longread_qc_run_filter = false longread_qc_skipqualityfilter = false
longread_qc_minlength = 1000 longread_qc_qualityfilter_minlength = 1000
longread_qc_keep_percent = 90 longread_qc_qualityfilter_keeppercent = 90
longread_qc_target_bases = 500000000 longread_qc_qualityfilter_targetbases = 500000000
save_preprocessed_reads = false save_preprocessed_reads = false

10
nextflow_schema.json
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@ -404,21 +404,21 @@
"type": "integer", "type": "integer",
"default": 30 "default": 30
}, },
"longread_qc_run_clip": { "longread_qc_skipadaptertrim": {
"type": "boolean" "type": "boolean"
}, },
"longread_qc_run_filter": { "longread_qc_skipqualityfilter": {
"type": "boolean" "type": "boolean"
}, },
"longread_qc_minlength": { "longread_qc_qualityfilter_minlength": {
"type": "integer", "type": "integer",
"default": 1000 "default": 1000
}, },
"longread_qc_keep_percent": { "longread_qc_qualityfilter_keeppercent": {
"type": "integer", "type": "integer",
"default": 90 "default": 90
}, },
"longread_qc_target_bases": { "longread_qc_qualityfilter_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_run_clip && !params.longread_qc_run_filter ) { 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_run_clip && params.longread_qc_run_filter ) { } 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())

1
workflows/taxprofiler.nf
View file

@ -22,7 +22,6 @@ 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_run_clip || params.longread_qc_run_filter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_run_clip or --longread_qc_run_filter 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'"