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https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 22:03:09 +00:00
Merge branch 'filtlong-in-tests' into json-schema
This commit is contained in:
commit
d19a473c59
7 changed files with 21 additions and 56 deletions
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@ -136,9 +136,9 @@ process {
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withName: FILTLONG {
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ext.args = [
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"--min_length ${params.longread_qc_minlength}",
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"--keep_percent ${params.longread_qc_keep_percent}",
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"--target_bases ${params.longread_qc_target_bases}"
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"--min_length ${params.longread_qc_qualityfilter_minlength}",
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"--keep_percent ${params.longread_qc_qualityfilter_keeppercent}",
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"--target_bases ${params.longread_qc_qualityfilter_targetbases}"
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]
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.join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
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@ -26,6 +26,7 @@ params {
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_qc = true
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perform_longread_qc = true
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shortread_qc_mergepairs = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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@ -26,6 +26,7 @@ params {
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_qc = true
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perform_longread_qc = true
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shortread_qc_mergepairs = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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@ -58,18 +58,18 @@ params {
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perform_shortread_qc = false
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shortread_qc_tool = 'fastp'
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shortread_qc_skipadaptertrim = false
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shortread_qc_mergepairs = false
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shortread_qc_mergepairs = true
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shortread_qc_excludeunmerged = false
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shortread_qc_adapter1 = null
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shortread_qc_adapter2 = null
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shortread_qc_minlength = 15
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perform_longread_qc = false
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longread_qc_run_clip = false
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longread_qc_run_filter = false
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longread_qc_minlength = 1000
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longread_qc_keep_percent = 90
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longread_qc_target_bases = 500000000
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perform_longread_qc = false
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longread_qc_skipadaptertrim = false
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longread_qc_skipqualityfilter = false
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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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save_preprocessed_reads = false
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@ -10,11 +10,7 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": [
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"input",
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"databases",
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"outdir"
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],
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"required": ["input", "databases", "outdir"],
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"properties": {
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"input": {
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"type": "string",
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@ -83,10 +79,7 @@
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"shortread_qc_tool": {
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"type": "string",
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"default": "fastp",
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"enum": [
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"fastp",
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"adapterremoval"
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],
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"enum": ["fastp", "adapterremoval"],
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"fa_icon": "fas fa-tools",
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"description": "Specify which tool to use for read QC"
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},
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@ -131,11 +124,7 @@
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"shortread_complexityfilter_tool": {
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"type": "string",
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"default": "bbduk",
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"enum": [
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"bbduk",
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"prinseqplusplus",
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"fastp"
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],
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"enum": ["bbduk", "prinseqplusplus", "fastp"],
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"fa_icon": "fas fa-hammer",
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"description": "Specify which tool to use for complexity filtering"
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},
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@ -165,10 +154,7 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": [
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"entropy",
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"dust"
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],
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"enum": ["entropy", "dust"],
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"fa_icon": "fas fa-check-square",
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"description": "Specify the complexity filter mode for PRINSEQ++"
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},
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@ -323,15 +309,7 @@
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"diamond_output_format": {
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"type": "string",
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"default": "tsv",
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"enum": [
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"blast",
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"xml",
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"txt",
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"daa",
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"sam",
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"tsv",
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"paf"
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],
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"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
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"fa_icon": "fas fa-file",
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"description": "Specify output format from DIAMOND profiling."
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},
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@ -348,14 +326,7 @@
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"kaiju_taxon_rank": {
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"type": "string",
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"default": "species",
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"enum": [
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"phylum",
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"class",
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"order",
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"family",
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"genus",
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"species"
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],
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"enum": ["phylum", "class", "order", "family", "genus", "species"],
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"fa_icon": "fas fa-tag",
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"description": "Specify taxonomic rank to be displayed in Kaiju taxon table"
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},
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@ -540,14 +511,7 @@
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"description": "Method used to save pipeline results to output directory.",
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"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.",
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"fa_icon": "fas fa-copy",
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"hidden": true
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},
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"email_on_fail": {
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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_run_clip && !params.longread_qc_run_filter ) {
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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_run_clip && params.longread_qc_run_filter ) {
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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 +22,6 @@ 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_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"
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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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