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Merge branch 'filtlong-in-tests' into json-schema

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This commit is contained in:
James Fellows Yates 2022-08-30 14:33:19 +02:00
commit d19a473c59
7 changed files with 21 additions and 56 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" }

1
conf/test.config
View file

@ -26,6 +26,7 @@ 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
perform_shortread_complexityfilter = true
perform_shortread_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'
perform_shortread_qc = true
perform_longread_qc = true
shortread_qc_mergepairs = true
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true

14
nextflow.config
View file

@ -58,18 +58,18 @@ params {
perform_shortread_qc = false
shortread_qc_tool = 'fastp'
shortread_qc_skipadaptertrim = false
shortread_qc_mergepairs = false
shortread_qc_mergepairs = true
shortread_qc_excludeunmerged = false
shortread_qc_adapter1 = null
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_skipqualityfilter = false
longread_qc_qualityfilter_minlength = 1000
longread_qc_qualityfilter_keeppercent = 90
longread_qc_qualityfilter_targetbases = 500000000
save_preprocessed_reads = false

50
nextflow_schema.json
View file

@ -10,11 +10,7 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": [
"input",
"databases",
"outdir"
],
"required": ["input", "databases", "outdir"],
"properties": {
"input": {
"type": "string",
@ -83,10 +79,7 @@
"shortread_qc_tool": {
"type": "string",
"default": "fastp",
"enum": [
"fastp",
"adapterremoval"
],
"enum": ["fastp", "adapterremoval"],
"fa_icon": "fas fa-tools",
"description": "Specify which tool to use for read QC"
},
@ -131,11 +124,7 @@
"shortread_complexityfilter_tool": {
"type": "string",
"default": "bbduk",
"enum": [
"bbduk",
"prinseqplusplus",
"fastp"
],
"enum": ["bbduk", "prinseqplusplus", "fastp"],
"fa_icon": "fas fa-hammer",
"description": "Specify which tool to use for complexity filtering"
},
@ -165,10 +154,7 @@
"shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string",
"default": "entropy",
"enum": [
"entropy",
"dust"
],
"enum": ["entropy", "dust"],
"fa_icon": "fas fa-check-square",
"description": "Specify the complexity filter mode for PRINSEQ++"
},
@ -323,15 +309,7 @@
"diamond_output_format": {
"type": "string",
"default": "tsv",
"enum": [
"blast",
"xml",
"txt",
"daa",
"sam",
"tsv",
"paf"
],
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
"fa_icon": "fas fa-file",
"description": "Specify output format from DIAMOND profiling."
},
@ -348,14 +326,7 @@
"kaiju_taxon_rank": {
"type": "string",
"default": "species",
"enum": [
"phylum",
"class",
"order",
"family",
"genus",
"species"
],
"enum": ["phylum", "class", "order", "family", "genus", "species"],
"fa_icon": "fas fa-tag",
"description": "Specify taxonomic rank to be displayed in Kaiju taxon table"
},
@ -540,14 +511,7 @@
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"email_on_fail": {

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_skipqualityfilter) {
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_skipqualityfilter) {
ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
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_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'"