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Standardise QC parameter system and turn on both porechop/filtlong in tests

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This commit is contained in:
James Fellows Yates 2022-08-30 13:58:58 +02:00
parent 1821496a49
commit 2cc07183a0
7 changed files with 23 additions and 17 deletions
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6
conf/modules.config
View file

@ -136,9 +136,9 @@ process {
withName: FILTLONG {
ext.args = [
"--min_length ${params.longread_qc_minlength}",
"--keep_percent ${params.longread_qc_keep_percent}",
"--target_bases ${params.longread_qc_target_bases}"
"--min_length ${params.longread_qc_qualityfilter_minlength}",
"--keep_percent ${params.longread_qc_qualityfilter_keeppercent}",
"--target_bases ${params.longread_qc_qualityfilter_targetbases}"
]
.join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }

3
conf/test.config
View file

@ -26,6 +26,9 @@ params {
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_qc = true
perform_longread_qc = true
shortread_qc_mergepairs = true
longread_qc_skipadaptertrim = false
longread_qc_qualityfilter = true
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true

3
conf/test_noprofiling.config
View file

@ -26,6 +26,9 @@ params {
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_qc = true
perform_longread_qc = true
shortread_qc_mergepairs = true
longread_qc_skipadaptertrim = false
longread_qc_qualityfilter = true
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true

12
nextflow.config
View file

@ -64,12 +64,12 @@ params {
shortread_qc_adapter2 = null
shortread_qc_minlength = 15
perform_longread_qc = false
longread_qc_run_clip = false
longread_qc_run_filter = false
longread_qc_minlength = 1000
longread_qc_keep_percent = 90
longread_qc_target_bases = 500000000
perform_longread_qc = false
longread_qc_skipadaptertrim = false
longread_qc_qualityfilter = false
longread_qc_qualityfilter_minlength = 1000
longread_qc_qualityfilter_keeppercent = 90
longread_qc_qualityfilter_targetbases = 500000000
save_preprocessed_reads = false

10
nextflow_schema.json
View file

@ -404,21 +404,21 @@
"type": "integer",
"default": 30
},
"longread_qc_run_clip": {
"longread_qc_skipadaptertrim": {
"type": "boolean"
},
"longread_qc_run_filter": {
"longread_qc_qualityfilter": {
"type": "boolean"
},
"longread_qc_minlength": {
"longread_qc_qualityfilter_minlength": {
"type": "integer",
"default": 1000
},
"longread_qc_keep_percent": {
"longread_qc_qualityfilter_keeppercent": {
"type": "integer",
"default": 90
},
"longread_qc_target_bases": {
"longread_qc_qualityfilter_targetbases": {
"type": "integer",
"default": 500000000
},

4
subworkflows/local/longread_preprocessing.nf
View file

@ -14,7 +14,7 @@ workflow LONGREAD_PREPROCESSING {
ch_versions = 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_qualityfilter ) {
PORECHOP ( reads )
ch_processed_reads = PORECHOP.out.reads
@ -28,7 +28,7 @@ workflow LONGREAD_PREPROCESSING {
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
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_qualityfilter ) {
ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
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_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.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.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'"